Fusion proteins comprising modified alpha virus surface glycoproteins and tumor associated antigen and methods thereof

ABSTRACT

The present disclosure relates to fusion proteins that comprise one or more modified alpha virus surface glycoproteins and one or more tumor specific antigens. Also disclosed are fusion proteins that comprise one or more modified alpha virus surface glycoproteins and one or more viral specific antigens. Also disclosed are fusion proteins that comprise one or more modified alpha virus surface glycoproteins. It also relates to methods to activate the immune system in cancer patients to infiltrate and kill tumor cells or cells infected with a latent virus. The present disclosure provides a platform technology that elicits a faster, broader and stronger immune response using the fusion proteins.

RELATED APPLICATION

This application is a National Phase application under 35 U.S.C. § 371 of International Patent Application No. PCT/US2016/023203, filed Mar. 18, 2016, and claims the benefit of U.S. application Ser. No. 62/134,933, filed Mar. 18, 2015, all of which are incorporated by reference in their entireties. The International Application was published on Sep. 22, 2016 as International Publication No. WO 2016/149643 A2.

SEQUENCE LISTING

A sequence listing, created on Sep. 11, 2017 as the ASCII text file “10315_004071_US1_SEQLIST.txt” having a file size of 54.6 kilobytes, is incorporated herein by reference in its entirety.

1. FIELD

The present disclosure relates to fusion proteins that comprise one or more modified alpha virus surface glycoproteins and one or more tumor specific antigens. Also disclosed are fusion proteins that comprise one or more modified alpha virus surface glycoproteins and one or more viral specific antigens. Also disclosed are fusion proteins that comprise one or more modified alpha virus surface glycoproteins. It also relates to methods to activate the immune system in cancer patients to infiltrate and kill tumor cells or cells infected with a latent virus. The present disclosure provides a platform technology that elicits a faster, broader and stronger immune response using the fusion proteins.

2. BACKGROUND

Ovarian cancer is the leading cause of death from gynecological malignancy in the US (1). Unfortunately, most cases are not diagnosed until the disease has progressed to stage III or IV, at which point recurrence is common even after an initially successful response to surgery and chemotherapy (2). It has been shown, however, that patients whose tumors are infiltrated with lymphocytes have a significantly higher 5-year survival rate than those who do not (3), suggesting the immune system plays an important role in combating tumor growth and that immunotherapy could be a successful strategy for fighting this disease. It is also known that many cancers are caused by viral infections.

The immune system plays an important role in controlling and preventing the growth of aberrant tumor cells via a mechanism known as “cancer immunoediting” (4). Cytotoxic CD8 T cells and natural killer (NK) cells can recognize and destroy these cells as they arise. It has been shown that immunodeficient mice lacking these cell types have increased susceptibility to tumor formation (4). However, tumor cells can develop mutations that help them evade detection by the immune system and mature tumors are therefore often poorly immunogenic, which has hindered the successful translation of many of these therapies to human patients (4). Additionally, tumors can form a unique microenvironment that shields them from direct contact with lymphocytes.

However, some advances have been made that are able to circumvent the tumor's immunosuppressive nature. The immunotherapeutic antibodies Ipilimumab and Nivolumab have recently been approved for the treatment of certain cancers. These checkpoint inhibitors target and block the activity of the immunosuppressive receptors CTLA-4 (Ipilimumab) and PD-1 (Nivolumab) on T cells. These drugs are not without safety concerns however, as these immune suppressive mechanisms are important for controlling potentially dangerous autoimmune and allergic reactions. Chimeric antigen receptor (CAR) T cell therapy has shown strong potential for treating blood-based cancers such as B cell acute lymphoblastic leukemia (ALL). To generate CAR T cells, the patient's own T cells are harvested and genetically modified to express a receptor that will recognize a specific surface antigen on the tumor cell (5). This method circumvents the signaling pathways that typically occur between the T cell and the antigen presenting tumor cell, rendering them resistant to immunosuppression. Because it requires genetic engineering of the patients own cells and due to potentially dangerous side effects of cytokine-release syndrome that can occur (6), CAR T therapy requires close individual monitoring that would not be necessary with more traditional drug therapies. The ability of CAR T cells to fight solid tumors such as ovarian cancer is still being evaluated.

Another method for fighting cancer that has shown potential is the use of oncolytic viruses (OVs) or viral vectors. These viruses are thought to act by specifically infecting and killing cancer cells. As cancer cells are lysed, dendritic cells are able to pick up released tumor antigens and generate a better anti-tumor immune response. However, the viruses and viral vectors were found to accumulate in the lymph nodes or other organs and at locations other than the intended target tumor. Thus, there remains a need to provide a method for safe and effective cancer treatment and prevention that does not have the danger and drawback as discussed above.

3. SUMMARY

Described herein are fusion proteins comprising one or more tumor associated antigens and one or more modified alpha virus surface glycoproteins. Also described are the multimeric complexes, nucleic acids encoding the modified fusion proteins, amino acid sequences of the fusion proteins, antibodies to the fusion proteins, and uses thereof. In certain embodiments, the alpha virus is Sindbis alpha virus or chikungunya virus. In certain embodiments, the modified alpha virus surface glycoprotein is E1, E2 or 6K. In certain embodiments, the modified alpha virus surface glycoprotein is E1 and E2. In certain embodiments, provided herein are modified alpha virus polyprotein. In certain embodiments, the polyprotein is E3 or capsid protein. Provided herein are fusion proteins comprising one or more modified alpha virus surface glycoproteins and other proteins as disclosed in table 3 of the NCI Pilot Project to Prioritize Cancer Antigens Clin. Cancer Res 2009; 15:5323-5337. Also described herein is a recombinant fusion protein comprising a modified alpha virus surface glycoproteins and one or more genes or gene segments. In certain embodiments, the fusion proteins are encoded by a construct comprising gene or gene segments of the tumor associated antigen that are inserted internally or terminally of gene segments of the alpha virus surface glycoproteins. In certain embodiments, the gene or gene segments are one or more tumor associated antigens. In certain embodiments, the fusion protein is a monomer, complex, conjugate. In certain embodiments, the fusion protein is capable of forming a dimer, trimer or multimer.

Also described herein are fusion proteins comprising one or more viral antigens and one or more modified alpha virus surface glycoproteins.

Also described herein are methods of treatment or prevention of a disease by administration of the fusion protein comprising one or more tumor associated antigen and one or more modified alpha virus surface glycoproteins. In certain embodiment, the method disclosed herein is for the treatment of a subject to activate a suppressed immune system. In certain embodiments, the treatment is for cancer patients. In certain embodiments, the treatment comprises infiltrating and killing tumor cells. In certain embodiments, the treatment comprises killing latent viral infected cells.

In one embodiment, disclosed is a method for treating cancer in a subject, comprising administering to the subject in need thereof, a fusion protein wherein the fusion protein consists essentially of alpha virus surface membrane glycoprotein E1, E2 and at least one linker, wherein the fusion protein stimulates an immune response when administered to the subject.

Described herein is a kit containing the fusion protein for the prevention and treatment of diseases.

The methods disclosed comprises administration of a fusion protein comprising one or more tumor associated antigens and one or more modified alpha virus surface glycoproteins. In certain embodiments, the modified alpha virus surface glycoprotein is a monomer, complex, fusion, conjugate. In certain embodiments, the fusion protein is capable to form a dimer, trimer or multimer. The fusion protein comprising one or more tumor associated antigens and one or more modified alpha virus surface glycoprotein is useful for one or more of the following: (i) excite/activate the human immune system; (ii) stimulate/activate growth of human T cells; (iii) excite/activate human hemopoietic cells, including T cells, NK cells, B cells, dendritic cells, regulatory T cells, macrophages, erythrocytes, etc.; (iv) release T cells from anergy; (v) overcome breakpoint inhibition of T cells; (vi) treat or prevent cancer; and (vii) latent viral infected cells. In certain embodiments, the method comprises administration of the fusion protein comprising a tumor associated antigen and modified alpha virus surface glycoprotein to a subject in need thereof to: (i) excite/activate the human immune system; (ii) stimulate/activate growth of human T cells; (iii) excite/activate human hemopoietic cells, including T cells, NK cells, B cells, dendritic cells, regulatory T cells, macrophages, erythrocytes, etc.; (iv) release T cells from anergy; (v) overcome breakpoint inhibition of T cells; and (vi) treat or prevent cancer. In certain embodiment, the method disclosed herein is for the treatment of a subject to activate a suppressed immune system in cancer patients to infiltrate and kill tumor cells. In other embodiments, the fusion protein comprising one or more viral antigens and one or more modified alpha virus surface glycoprotein which is useful for killing latent viral infected cells.

4. BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-B The Structural Proteins of an Alpha Virus. (A) The cryo-EM density of Sindbis virus showing T=4 symmetry. The four E2 molecules in one asymmetric unit. These give rise to one trimeric spike on each icoshedral three-fold axis and one generally positioned spike. (B) Threading of the Sindbis virus structural polyprotein through an endoplasmic reticulum membrane showing the position of the capsid, E3, E2, 6K and E1 proteins. (Li, L. et al. Structural changes of envelope proteins during alphavirus fusion. Nature 468, 705-708 (2010)).

FIGS. 2A-B Domain structure of the glycoprotein spike. (A) Ribbon diagram of the p62-E1 heterodimer, E1 domains I, II and III are shown in red, yellow and blue, respectively, and the fusion loop (FL) in orange. E3 is colored white/grey and E2 domain A is colored cyan, B dark green, C pink and the β-ribbon dark purple. The N-finked glycans are shown in ball and stick, colored according to atom type, and labeled. The disulphides are depicted as green sticks. The black arrow (next to the pink and blue stars indicating the C termini of p62 and E1, respectively) points to the viral membrane. Inset, schematic diagram, with the heterodimer ‘plate’ drawn ‘untwisted’, showing how the domains are positioned with respect to one another and their connectivity. (B) p62 organization, oriented roughly at 90 degrees from a to show E3. (Voss J E, et al. Glycoprotein organization of chikungunya virus particles revealed by x-ray crystallography. Nature 468, 709-712 (2010)).

FIG. 3 Structure of engineered recombinant Sindbis VGP. Left, complete structural protein composition encoded by SINV. Right, engineered VGP lacking transmembrane domains and 6K region, linked with a Tumor Associated Antigen (TAA).

FIGS. 4A-C. Engineered Viral Glycoprotein Construct E2 E1 Dimer and TAA form spike trimer Transmembrane and 6K regions are removed and E2 and E1 are joined by a flexible linker. The E3 sequence acts as an ER targeting sequence and aids in E2/E1 dimerization. TAA is added to C-terminus of E1 with another flexible linker and a protease cleavage site. VGPs trimerized forming soluble spike carrying TAAs upon secretion from golgi.

FIG. 5 Amino acid sequence of an example of fusion protein E3-E2-linker-E1-TEV-linker-NY-ESO-1-6×His. E3-amino acid residues at positions 1-65; E2-amino acid residues at positions 66-429; linker-amino acid residues at positions 430-448; E1-amino acid residues at positions 449-854; TEV-linker-amino acid residues at positions 855-876; and NY-ESO-1 peptide fragment amino acid residues at positions 877-978; 6×His-amino acid residues at positions 979-984. Bolded N is glycosylation sites: amino acid residues at positions 261, 383, 587 and 693.

FIG. 6 Nucleic acid sequence of an example of fusion protein E3-E2-linker-E1-TEV-linker-NY-ESO-1-6×His

FIG. 7 Western Blot of purified fusion protein Supernatant was harvested from 100 ml culture and protein was purified by Ni affinity chromatography. Predicted molecular weight: 106.8 kDa

Lane M2: Easy western marker

Lane 1: Medium of cell lysate

Lane 2: Flow through

Lane 3: Eluted with 20 mM imidazole

Lane 4: Eluted with 500 mM imidazole

Lane 5: Resins after elution

Antibody: anti-His antibody (Genscript, Cat. No. A00186)

FIGS. 8A-F. Amino acid sequences of antigens useful for making the presently disclosed fusion proteins (SEQ ID NOS: 3-11).

FIG. 9. Full Sindbis structural protein sequence (Capsid, E3, E2 Ectodomain, E2 Transmembrane Domain, 6K, E1 Ectodomain, E1 Transmembrane Domain) SEQ ID NO:12.

4.1 DEFINITIONS

As used herein, the term “alphavirus” has its conventional meaning in the art, and includes the various species such as VEE, SFV, Sindbis, Ross River Virus, Western Equine Encephalitis Virus, Eastern Equine Encephalitis Virus, Chikungunya, S.A. AR86, Everglades virus, Mucambo, Barmah Forest Virus, Middelburg Virus, Pixuna Virus, O'nyong-nyong Virus, Getah Virus, Sagiyama Virus, Bebaru Virus, Mayaro Virus, Una Virus, Aura Virus, Whataroa Virus, Banbanki Virus, Kyzylagach Virus, Highlands J Virus, Fort Morgan Virus, Ndumu Virus, and Buggy Creek Virus. In certain embodiments, the alphaviruses used in the constructs and methods of the present disclosure are VEE, S.AAR86, Sindbis (e.g. TR339, see U.S. Pat. No. 6,008,035), and SFV.

The term adjuvant refers to any substance whose admixture with an administered immunogenic determinant/antigen/nucleic acid construct increases or otherwise modifies the immune response to said determinant.

The term amino acid refers to synthetic or naturally occurring amino carboxylic acid, including any amino acid occurring in peptides and polypeptides including proteins and enzymes synthesized in vivo thus including modifications of the amino acids. The term amino acid is herein used synonymously with the term “amino acid residue” which is meant to encompass amino acids as stated which have been reacted with at least one other species, such as 2, for example 3, such as more than 3 other species. The generic term amino acid comprises both natural and non-natural amino acids any of which may be in the “D” or “L” isomeric form.

The term antibody refers to immunoglobulin molecules and active portions of immunoglobulin molecules. Antibodies are for example intact immunoglobulin molecules or fragments thereof retaining the immunologic activity.

The term antigen refers to any substance that can bind to a clonally distributed immune receptor (T-cell or B-cell receptor). Usually a peptide, polypeptide or a multimeric polypeptide. Antigens are preferably capable of eliciting an immune response.

The term boost used herein as to boost by a booster shot or dose is to give an additional dose of an immunizing agent, such as a vaccine, given at a time after the initial dose to sustain the immune response elicited by the previous dose of the same agent.

The term carrier refers to an entity or compound to which antigens are coupled to aid in the induction of an immune response.

The term fusion protein refers to a genetically engineered protein that is encoded by a nucleotide sequence made by a joining together two or more complete or partial genes or a series of nucleic acids. Alternatively, a fusion protein may be made by joining together two or more of heterologous peptides.

The term cytokine refers to growth or differentiation modulator, used non-determinative herein. In addition to the cytokines, adhesion or accessory molecules, or any combination thereof, may be employed alone or in combination with the cytokines.

The term Cytotoxic T lymphocytes refers to a sub group of T-cells expressing CD8 along with the T-cell receptor and therefore able to respond to antigens presented by class I molecules.

The term delivery vehicle refers to an entity whereby a nucleotide sequence or polypeptide or both can be transported from at least one media to another.

The term fragment refers to a non-full length part of a nucleic acid polypeptide.

The term subject refers to any species or subspecies of bird, mammal, human, non-human, fish, amphibian, or reptile.

The term isolated used in connection with nucleic acids, polypeptides, and antibodies refers to these having been identified and separated and/or recovered from a component of their natural, typically cellular, environment.

The term nucleic acids, polypeptides, and antibodies are preferably isolated, and vaccines and other compositions of the invention preferably comprise isolated nucleic acids, polypeptides or isolated antibodies.

The term MHC or Major histocompatibility complex refers to two main subclasses of MHC, Class I and Class II.

The term nucleic acid refers to a chain or sequence of nucleotides that convey genetic information. Nucleic acid construct refers to a genetically engineered nucleic acid. Typically comprising several elements such as genes or fragments of same, promoters, enhancers, terminators, polyA tails, linkers, polylinkers, operative linkers, multiple cloning sites (MCS), markers, STOP codons, other regulatory elements, internal ribosomal entry sites (IRES) or others.

The term operative linker refers to a sequence of nucleotides or amino acid residues that bind together two parts of a nucleic acid construct or fusion polypeptide in a manner securing the biological processing of the nucleic acid or polypeptide.

The term pathogen refers to a specific causative agent of disease, especially a biological agent such as a virus, bacteria, prion or parasite that can cause disease to its host, also referred to as an infective agent.

The term “cancer” or “tumor” refers to a neoplasm or tumor resulting from abnormal uncontrolled growth of cells. The term “cancer” encompasses a disease involving both pre-malignant and malignant cancer cells. In some embodiments, cancer refers to a localized overgrowth of cells that has not spread to other parts of a subject, i.e., a benign tumor. In other embodiments, cancer refers to a malignant tumor, which has invaded and destroyed neighboring body structures and spread to distant sites. In yet other embodiments, the cancer is associated with a specific cancer antigen.

As used herein, the term “effective amount” refers to the amount of a therapy that is sufficient to result in the prevention of the development, recurrence, or onset of cancer and one or more symptoms thereof, to enhance or improve the prophylactic effect(s) of another therapy, reduce the severity, the duration of cancer, ameliorate one or more symptoms of cancer, prevent the advancement of cancer, cause regression of cancer, and/or enhance or improve the therapeutic effect(s) of another therapy. In one embodiment, the amount of a therapy is effective to achieve one, two, three or more of the following results following the administration of one, two, three or more therapies: (1) a stabilization, reduction or elimination of the cancer stem cell population; (2) a stabilization, reduction or elimination in the cancer cell population; (3) a stabilization or reduction in the growth of a tumor or neoplasm; (4) an impairment in the formation of a tumor; (5) eradication, removal, or control of primary, regional and/or metastatic cancer; (6) a reduction in mortality; (7) an increase in disease-free, relapse-free, progression-free, and/or overall survival, duration, or rate; (8) an increase in the response rate, the durability of response, or number of patients who respond or are in remission; (9) a decrease in hospitalization rate; (10) a decrease in hospitalization lengths; (11) the size of the tumor is maintained and does not increase or increases by less than 10%, preferably less than 5%, preferably less than 4%, preferably less than 2%; (12) an increase in the number of patients in remission; (13) an increase in the length or duration of remission; (14) a decrease in the recurrence rate of cancer; (15) an increase in the time to recurrence of cancer; and (16) an amelioration of cancer-related symptoms and/or quality of life.

The term peptide refers to plurality of covalently linked amino acid residues defining a sequence and linked by amide bonds. The term is used analogously with oligopeptide and polypeptide. The natural and/or non-natural amino acids may be linked by peptide bonds or by non-peptide bonds. The term peptide also embraces post-translational modifications introduced by chemical or enzyme-catalyzed reactions, as are known in the art. The term can refer to a variant or fragment of a polypeptide.

The term pharmaceutical carriers, excipients, or stabilizers' are non-toxic to the cell or individual being exposed thereto at the dosages and concentrations employed. Often the physiologically acceptable carrier is an aqueous pH buffered solution. Examples of physiologically acceptable carriers include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN™, polyethylene glycol (PEG), and PLURONICS™.

The term promoter refers to a binding site in a DNA chain at which RNA polymerase binds to initiate transcription of messenger RNA by one or more nearby structural genes.

The term signal peptide refers to a short sequence of amino acids that determine the eventual location of a protein in the cell, also referred to as sorting peptide.

The term surfactant refers to a surface active agent capable of reducing the surface tension of a liquid in which it is dissolved. A surfactant is a compound containing a polar group which is hydrophilic and a non-polar group which is hydrophobic and often composed of a fatty chain.

The term vaccine refers to a substance or composition capable of inducing an immune response in an animal. Also referred to as an immunogenic composition. An immune response being an immune response (humoral/antibody and/or cellular) inducing memory in an organism, resulting in the infectious agent, being met by a secondary rather than a primary response, thus reducing its impact on the host organism. A vaccine may be given as or prophylactic and/or therapeutic medicament. The composition may comprise one or more of the following: VGP conjugated to one or more tumor associated antigen(s), nucleic acid constructs comprising VGP operatively linked to one or more antigens, carriers, adjuvants and pharmaceutical carriers.

The term variant refers to a nucleic acid or polypeptide that displays a certain degree of sequence homology/identity to a given reference nucleic acid or polypeptide but is not identical to said reference nucleic acid or polypeptide.

5. DETAILED DESCRIPTION 5.1 Fusion Protein Comprising Modified Alphavirus Glycoproteins and Antigens

Like all alphaviruses, the Sindbis genome encodes for 4 nonstructural proteins (nsP1-4) responsible for RNA replication, and 5 structural proteins (capsid, E3, E2, 6K, and E1). The structural proteins are expressed as a single polyprotein that is cleaved by cellular proteases to generate the mature proteins (see FIG. 1). The capsid protein forms an internal core surrounding the viral genome and interacts with the cytoplasmic tail of the E2 envelope glycoprotein (7). The E3 protein acts a signal sequence for pE2, the precursor protein composed of E3 and E2, mediates proper E2 folding, and is necessary for the heterodimerization of E2 with E1 (7). During protein processing in the golgi, E3 is cleaved by furin and shed upon virus budding from the cell (7). Sindbis Virus (“SINV”) E2 is a transmembrane glycoprotein with 2 N-linked glycosylation sites at 196 and 318 (8). The 6K protein acts as a signal sequence for E1, is cleaved from E1 and E2 by signal peptidase, and is minimally present in the mature virion. SINV E1 is a transmembrane glycoprotein with 2 N-linked glycosylation sites at 139 and 245 (8). As the virus buds from the cell, the capsid is contained within the viral envelope derived from the host cell plasma membrane. The E2/E1 heterodimer exists as a trimeric spike on the surface of the viral envelope. The E2 region is responsible for interacting with receptors on target cells, while E1 triggers membrane fusion under the low pH conditions of late endosomes and lysosomes (8).

Described herein is a fusion protein comprising modified viral glycoproteins (VGPs), the E1 and E2 proteins expressed together as a single recombinant protein (see FIG. 3) that are conjugated to tumor specific antigens forming a fusion protein VGP-TAA for therapy. In specific embodiments, the fusion protein does not contain transmembrane protein, 6K regions and non-structural proteins. In specific embodiments, the expression vector that expresses the fusion protein is not a viral vector. In one embodiment, the fusion protein has the amino acid sequence of SEQ ID NO: 1. In certain embodiments, the fusion protein has the amino acid sequence of SEQ ID NO:1 with the following modifications: (1) deletion of the following amino acid residues: 1-65, 979-978. The fusion protein is a recombinant protein that is encoded by a nucleotide having a nucleotide sequence of the viral surface membrane glycoprotein that is operatively linked to one or more tumor associated antigen. In certain embodiments, the one or more tumor associated antigens are disclosed in table 3 of the NCI Pilot Project to Prioritize Cancer Antigens Clin. Cancer Res 2009; 15:5323-5337.

In certain embodiments, the tumor associated antigen portion of the fusion protein may have an amino acid sequence having at least a % identity to SEQ ID NOs: 3-11. In certain embodiments, the tumor associated antigen portion of the fusion protein may have an amino acid sequence having at least a % identity to SEQ ID NOs: 1 at amino acid positions 877-978.

In certain embodiments, the tumor associated antigen includes at least 7, 8, 9, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more consecutive amino acids of any of SEQ ID NOs: 3-11, wherein the consecutive amino acids is immunogenic.

In certain embodiments, the tumor associated antigen comprises 10-20, 20-30, 30-50, 50-150, 150-200, 200-400, 400-500 amino acids from SEQ ID NOs: 3-11. In certain embodiments, the tumor associated antigen does not comprise a full length protein from SEQ ID Nos: 3-11.

In certain embodiments, the tumor associated antigen has less than 1200 amino acids, less than 1100 amino acids, less than 1000 amino acids, less than 950 amino acids, less than 900 amino acids, less than 850 amino acids, less than 800 amino acids, less than 750 amino acids, less than 700 amino acids, less than 650 amino acids, less than 600 amino acids, less than 590 amino acids, or less than 580 amino acids of the protein from SEQ ID Nos: 3-11.

Tumor associated antigen fragments from SEQ ID NOs 3-11 discussed above include, without limitation, are immunogenic fragments that, when administered to a subject in a suitable composition which can include an adjuvant (including without limitation any of the adjuvants listed or discussed in the section “Immunogenic compositions and medicaments” below), or a suitable carrier coupled to the polypeptide, induces an antibody or T-cell mediated immune response that recognizes the isolated full length polypeptide SEQ ID Nos 3-11, respectively, from which the immunogenic fragment is derived.

Tumor associated antigen may, compared to any one of SEQ ID Nos 3-11, include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, etc.) amino acid substitutions, such as conservative substitutions (i.e. substitutions of one amino acid with another which has a related side chain). Genetically-encoded amino acids are generally divided into four families: (1) acidic i.e. aspartate, glutamate; (2) basic i.e. lysine, arginine, histidine; (3) non-polar i.e. alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan; and (4) uncharged polar i.e. glycine, asparagine, glutamine, cysteine, serine, threonine, tyrosine. Phenylalanine, tryptophan, and tyrosine are sometimes classified jointly as aromatic amino acids. In general, substitution of single amino acids within these families does not have a major effect on the biological activity.

A polypeptide may include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, etc.) single amino acid deletions relative to any one of SEQ ID Nos 3-11. Similarly, a polypeptides may include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, etc.) insertions (e.g. each of 1, 2, 3, 4 or 5 amino acids) relative to any one of SEQ ID Nos 3-11.

Deletions or substitutions may be at the N-terminus and/or C-terminus, or may be between the two termini. Thus a truncation is an example of a deletion. Truncations may involve deletion of up to 40 (or more) amino acids at the N-terminus and/or C-terminus.

In general, when a polypeptide of the invention comprises a sequence that is not identical to a complete sequence of SEQ ID NOs 3-11 (e.g. when it comprises a sequence listing with <100% sequence identity thereto, or when it comprises a fragment thereof) it is preferred that the polypeptide can elicit an antibody that recognises a polypeptide consisting of the complete SEQ ID sequence i.e. the antibody binds to one or more of said SEQ ID Nos 3-11. Such antibody may bind specifically to SEQ ID Nos 3-11, respectively while not binding to other proteins that are not homologs with affinity significantly higher than the antibody's non-specific affinity to human serum albumin as a non-specific binding reference standard.

A polypeptide of the invention may include a metal ion e.g. a metal ion that is coordinated by one or more amino acids in the polypeptide chain. For instance, the polypeptide may include a monovalent, divalent or trivalent metal cation. Divalent cations are typical, such as Mn2+, Fe2+, Co2+, Ni2+, Cu2+, etc. The divalent cation is preferably Zn2+.

Polypeptides disclosed herein can take various forms (e.g. native, fusions, glycosylated, non-glycosylated, lipidated, non-lipidated, phosphorylated, non-phosphorylated, myristoylated, non-myristoylated, monomeric, multimeric, particulate, denatured, etc.). For instance, a polypeptide of the invention may have a lipidated N-terminal cysteine.

Polypeptides disclosed herein can be prepared by various means (e.g. recombinant expression, purification from cell culture, chemical synthesis, etc.). Recombinantly-expressed proteins are preferred.

Polypeptides disclosed herein are preferably provided in purified or substantially purified form i.e. substantially free from other polypeptides (e.g. free from naturally-occurring polypeptides), particularly from other E. coli or host cell polypeptides, and are generally at least about 50% pure (by weight), and usually at least about 90% pure i.e. less than about 50%, and more preferably less than about 10% (e.g. 5%) of a composition is made up of other expressed polypeptides. Thus the antigens in the compositions are separated from the whole organism with which the molecule is expressed.

An epitope within a tumor associated antigen from a peptide fragment may be a B-cell epitope and/or a T-cell epitope. Such epitopes can be identified empirically (e.g. using PEPSCAN or similar methods), or they can be predicted (e.g. using the Jameson-Wolf antigenic index, matrix-based approaches, MAPITOPE, TEPITOPE, neural networks, OptiMer & EpiMer, ADEPT, Tsites, hydrophilicity, antigenic index, etc.). Epitopes are the parts of an antigen that are recognised by and bind to the antigen binding sites of antibodies or T-cell receptors, and they may also be referred to as “antigenic determinants”.

Any of the polypeptides disclosed herein have utility as components of vaccines. Thus in another embodiment, the isolated or recombinant polypeptide will be with an adjuvant.

In one embodiment, the fusion protein comprises one or more antigenic proteins or peptide or fragment of an antigenic protein, which protein is a tumor associated antigen. Many proteins have been identified and linked to certain types of cancer; these are referred to as tumor associated antigens. In general, any antigen that is found to be associated with cancer tumors may be used. In certain embodiments, the tumor associated antigen is WT1 (UniProt Knowledgebase, MUC1 (P15941), LMP2 (P13285), HPV16 E6(P03126) and E7(P03129), HPV18 (E6-P06463) and E7(P06788), RGL4 (Q8IZJ4), EGFRvIII (P0533), HER-2/neu (P04626), MAGE A3 (Q53EX0), PSMA (Q04609), CEA (P06731), MelanA/MART (Q16655), gp100 (P40967), Proteinase3 (PR1) (P24158), bcr-abl fusion, bcr (P11274), abl (P00519), Tyrosinase (P14679), Survivin (015392), PSA (P07288), hTERT (014746), EphA2 (P29317), PAP (P15309), ML-IAP (Q96CA5), AFP (P02771), EpCAM (P16422), TMPRSS2/ERG fusion, TMPRSS2 (015393), ERG (P11308), PAX3 (P23760), ALK (Q9UM73), Androgen receptor (P10275), Cyclin B1 (P14635), MYCN (P04198), RhoC (P08134), TRP-2 (P40126), Mesothelin (Q13421), PSCA (043653), MAGE A1 (P43355), CYP1B1 (Q16678), PLAC1 (Q9HBJ0), BORIS (Q8NI51), NY-BR-1 (Q9BXX3), RGS5 (O15539), SART3 (Q15020), Carbonic anhydrase IX (Q16790), PAX5 (Q02548), OY-TES1 (Q8NEB7), Sperm protein 17 (Q15506), LCK (P06239), HMWMAA (Q6UVK1), AKAP-4 (Q5JQC9), SSX2 (Q16385), XAGE 1 (Q9HD64), Legumain (Q99538), Tie 2 (Q02763), VEGFR2 (P35968), PDGFR-β (P09619), and Fos-related antigen 1 (P15407).

In certain embodiments, one or more of the alpha virus surface membrane glycoproteins is operatively linked to one or more tumor associated antigen. In one embodiment, the tumor specific antigen is the primary antigenic region of the cancer-testis antigen NY-ESO-1. In certain embodiments, the tumor specific antigen includes the list of target human TAAs for cancer immunotherapy (9). In a specific embodiment, the SINV VGP recombinant protein is conjugated to the primary antigenic region of the NY-ESO-1 protein to form a fusion protein.

In certain embodiments, additional N-linked glycosylation sites may be engineered into the viral glycoprotein. N-linked glycans are attached to an asparagine side chain that is present as a part of Asparagine-X-Serine/Threonine sequence, where X is any amino acid except proline.

The disclosure also relates to a nucleic acid construct encoding a fusion protein comprising one or more tumor associated antigen and one or more alpha virus surface membrane glycoprotein having the amino acid sequence identified in SEQ ID NO: 1 or a fragment thereof. In certain embodiments, the fragment has 40-80, 80-150, 150-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-850, 850-900 amino acid residues. In certain embodiments, the fragment is at least 85%, 90%, 95%, 99% identical to SEQ NO: 2. In certain embodiments, the tumor associated antigens are full length proteins. In certain embodiments, the tumor associated antigens are fragments of a full length protein. In certain embodiments, the fragment has 5-10, 10-20, 20-30, 30-40, 40-80, 80-150, 150-200, 200-300, 300-400, 400-500, 500-600 amino acid residues. In certain embodiments, the fragment is at least 85%, 90%, 95%, 99% identical to wild type tumor associated antigen. The identity/homology between amino acid sequences may be calculated using well known scoring matrices such as any one of BLOSUM 30, BLOSUM 40, BLOSUM 45, BLOSUM 50, BLOSUM 55, BLOSUM 60, BLOSUM 62, BLOSUM 65, BLOSUM 70, BLOSUM 75, BLOSUM 80, BLOSUM 85, and BLOSUM 90.

In certain embodiments, the tumor associated antigen is a polypeptide fragment that is at least 10 consecutive amino acids of any of SEQ ID NOS: 3-11, wherein the polypeptide fragment comprises at least 10 consecutive amino acids is immunogenic and the immunogenic polypeptide fragment comprises less than 1100 amino acids of the polypeptide of SEQ ID Nos: 3-11.

In one embodiment, disclosed is an isolated or recombinant fusion protein consisting essentially of alpha virus surface membrane glycoproteins E1, E2 and optionally E3, a linker and at least one tumor associated antigen, wherein the fusion protein stimulates an immune response when administered to a subject. In one embodiment, the fusion protein of comprises an amino acid sequence having at least 98% identity to SEQ ID NO: 1. In one embodiment, the fusion protein comprises at least amino acid residues at positions 66-978 of SEQ ID NO:1. In one embodiment, the fusion protein is encoded by a nucleic acid molecule having at least 95% identity to SEQ ID NO: 2. In one embodiment, the fusion protein further comprising a deletion of amino acid residues at (i) positions 1-65; (ii) positions 979-984; or (iii) positions 1-65 and 979-984, of SEQ ID NO:1. In one embodiment, the E2 comprises an amino acid sequence that is at least 300 amino acid in length and has at least 95% sequence identity to SEQ ID NO:1 at positions 66-429. In one embodiment, the E1 comprises an amino acid sequence that is at least 300 amino acid in length and has at least 95% sequence identity to SEQ ID NO:1 at positions 449-854. In one embodiment, the tumor associated antigen is a polypeptide fragment that is at least 10 consecutive amino acids of any of SEQ ID NOS: 3-11, wherein the polypeptide fragment comprises at least 10 consecutive amino acids is immunogenic and the immunogenic polypeptide fragment comprises less than 1100 amino acids of the polypeptide of SEQ ID Nos: 3-11.

One skilled in the art would also know that the above can be applied to viral antigens. Thus, in certain embodiments, the tumor associated antigens are replaced by viral antigens. In certain embodiments, the fusion protein comprises one or more viral antigens and one or more alpha virus surface membrane glycoproteins. In certain embodiments, the viral antigen is HSV-1 glycoprotein B (P06437), glycoprotein E (P04488), HIV gag-pol (P04585), chickenpox (Varicella zoster) glycoprotein B (Q4JR05) or glycoprotein E (Q9J3M8).

5.2 Method of Making VGP-TAA

Provided herein is a process for producing a fusion protein, comprising the step of culturing a host cell transformed with nucleic acid encoding the fusion protein under conditions which induce polypeptide expression. The polypeptide may then be purified e.g. from culture supernatants.

The invention provides a process for producing a polypeptide of the invention, comprising the step of synthesizing at least part of the polypeptide by chemical means.

Any and all of the foregoing proteins, polypeptides, hybrid polypeptides, epitopes and immunogenic fragments may be in any one of a number of forms including, without limitation, recombinant, isolated or substantially purified (from materials co-existing with such proteins, polypeptides, hybrid polypeptides, epitopes and immunogenic fragments in their natural state).

In one aspect, the fusion protein as disclosed herein is encoded by a nucleic acid construct comprising one or more viral surface membrane glycoproteins operatively linked to one or more tumor associated antigen. The fusion protein is a recombinant protein that is encoded by a nucleotide having a nucleotide sequence of the viral surface membrane glycoprotein that is operatively linked to one or more tumor associated antigen. In one embodiment, the nucleic acid construct is an expression vector. In one embodiment, the expression vector is non-viral, viral or a plasmid. In certain embodiments, the expression vector comprises genes or fragment of genes, promoters, enhancers, termination signals, poly-A tails, linkers, polylinkers, operative linkers, multiple cloning sites, markers, STOP codons, internal ribosomal entry sites, host homologous sequences for integration or other defined elements. Methods for engineering nucleic acid constructs are well known in the art (see, e.g., Molecular Cloning: A Laboratory Manual, Sambrook et al, eds., Cold Spring Harbor Laboratory, 2nd Edition, Cold Spring Harbor, N.Y., 1989).

In some embodiments, nucleic acid of the invention hybridizes to a target under low stringency conditions; in other embodiments it hybridizes under intermediate stringency conditions; in preferred embodiments, it hybridizes under high stringency conditions. An exemplary set of low stringency hybridization conditions is 50° C. and 10×SSC. An exemplary set of intermediate stringency hybridization conditions is 55° C. and 1×SSC. An exemplary set of high stringency hybridization conditions is 68° C. and 0.1×SSC.

The invention includes nucleic acid comprising sequences complementary to these sequences (e.g. for antisense or probing, or for use as primers).

Nucleic acids of the invention can be used in hybridization reactions (e.g. Northern or Southern blots, or in nucleic acid microarrays or ‘gene chips’) and amplification reactions (e.g. PCR, SDA, SSSR, LCR, TMA, NASBA, etc.) and other nucleic acid techniques.

Nucleic acid according to the invention can take various forms (e.g. single-stranded, double-stranded, vectors, primers, probes, labelled etc.). Nucleic acids of the invention may be circular or branched, but will generally be linear, Unless otherwise specified or required, any embodiment of the invention that utilizes a nucleic acid may utilize both the double-stranded form and each of two complementary single-stranded forms which make up the double-stranded form. Primers and probes are generally single-stranded, as are antisense nucleic acids.

Nucleic acids of the invention are preferably provided in purified or substantially purified form i.e. substantially free from other nucleic acids (e.g. free from naturally-occurring nucleic acids), particularly from host cell nucleic acids, generally being at least about 50% pure (by weight), and usually at least about 90% pure.

Nucleic acids of the invention may be prepared in many ways e.g. by chemical synthesis (e.g. phosphoramidite synthesis of DNA) in whole or in part, by digesting longer nucleic acids using nucleases (e.g. restriction enzymes), by joining shorter nucleic acids or nucleotides (e.g. using ligases or polymerases), from genomic or cDNA libraries, etc.

Nucleic acid of the invention may be attached to a solid support (e.g. a bead, plate, filter, film, slide, microarray support, resin, etc.). Nucleic acid of the invention may be labelled e.g. with a radioactive or fluorescent label, or a biotin label. This is particularly useful where the nucleic acid is to be used in detection techniques e.g. where the nucleic acid is a primer or as a probe.

The term “nucleic acid” includes in general means a polymeric form of nucleotides of arty length, which contain deoxyribonucleotides, ribonucleotides, and/or their analogs. It includes DNA, RNA, DNA/RNA hybrids. It also includes DNA or RNA analogs, such as those containing modified backbones (e.g. peptide nucleic acids (PNAs) or phosphorothioates) or modified bases. Thus the invention includes mRNA, tRNA, rRNA, ribozymes, DNA, cDNA, recombinant nucleic acids, branched nucleic acids, plasmids, vectors, probes, primers, etc. Where nucleic acid of the invention takes the form of RNA, it may or may not have a 5′ cap.

Nucleic acids of the invention may be part of a vector i.e. part of a nucleic acid construct designed for transduction/transfection of one or more cell types. Vectors may be, for example, “cloning vectors” which are designed for isolation, propagation and replication of inserted nucleotides, “expression vectors” which are designed for expression of a nucleotide sequence in a host cell, “viral vectors” which is designed to result in the production of a recombinant virus or virus-like particle, or “shuttle vectors”, which comprise the attributes of more than one type of vector. Preferred vectors, are plasmids, as mentioned above. A “host cell” includes an individual cell or cell culture which can be or has been a recipient of exogenous nucleic acid. Host cells include progeny of a single host cell, and the progeny may not necessarily be completely identical (in morphology or in total DNA complement) to the original parent cell due to natural, accidental, or deliberate mutation and/or change. Host cells include cells transfected or infected in vivo or in vitro with nucleic acid of the invention.

Where a nucleic acid is DNA, it will be appreciated that “U” in a RNA sequence will be replaced by in the DNA. Similarly, where a nucleic acid is RNA, it will be appreciated that “T” in a DNA sequence will be replaced by “U” in the RNA.

The term “complement” or “complementary” when used in relation to nucleic acids refers to Watson-Crick base pairing. Thus the complement of C is G, the complement of G is C, the complement of A is T (or U), and the complement of T (or U) is A. It is also possible to use bases such as I (the purine inosine) e.g. to complement pyrimidines (C or T).

Nucleic acids of the invention can be used, for example: to produce polypeptides; as hybridization probes for the detection of nucleic acid in biological samples; to generate additional copies of the nucleic acids; to generate ribozymes or antisense oligonucleotides; as single-stranded DNA primers or probes; or as triple-strand forming oligonucleotides.

The invention provides a process for producing nucleic acid of the invention, wherein the nucleic acid is synthesized in part or in whole using chemical means.

The invention provides vectors comprising nucleotide sequences of the invention (e.g. cloning or expression vectors)) and host cells transformed with such vectors.

Nucleic acid amplification according to the invention may be quantitative and/or real-time.

For certain embodiments of the invention, nucleic acids are preferably at least 7 nucleotides in length (e.g. 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 225, 250, 275, 300 nucleotides or longer).

For certain embodiments of the invention, nucleic acids are preferably at most 500 nucleotides in length (e.g. 450, 400, 350, 300, 250, 200, 150, 140, 130, 120, 110, 100, 90, 80, 75, 70, 65, 60, 55, 50, 45, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15 nucleotides or shorter).

Primers and probes of the invention, and other nucleic acids used for hybridization, are preferably between 10 and 30 nucleotides in length (e.g. 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides).

In certain embodiments, the disclosed nucleic acid construct that encodes the fusion protein comprises one or more alpha virus surface membrane glycoprotein conjugated to one or more tumor associated antigen through an operative linker. In one embodiment, the linker is a direct link. In one embodiment, the linker is a spacer region. By the term operative linker is understood a sequence of nucleotides or amino acid residues that bind together two parts of a nucleic acid construct or fusion protein in a manner securing the biological processing of the nucleic acid or the protein. If the operative linker is a direct link, the two nucleic acids each encoding either an open reading frame or a fragment of an open reading frame are placed immediately adjacent to each other and thereby also in frame. If the operative linker is mediated by a spacer region, a series of nucleotides are inserted between the nucleotides encoding the one or more alpha virus surface membrane glycoprotein and the one or more tumor associated antigen. In certain embodiments, the operative linker comprises at least one polylinker or multiple cloning site (MCS).

Examples of nucleic acid constructs are provided in FIG. 6, as well as in the sequences identified as SEQ ID NO:2. The partial vector sequences of SEQ ID NO: 1 were generated by subcloning various elements as described in the above. These partial sequences are all inserted into pUC57, then transferred to the pFastBac1. See GenBank accession number AY598466.

In one embodiment, the transmembrane and 6K regions are removed and E2 and E1 are joined by a flexible linker. The E3 sequence acts as an ER targeting sequence and aids in E2/E1 dimerization. TAA is added to C-terminus of E1 with another flexible linker and a protease cleavage site. VGPs trimerize forming soluble spike carrying TAAs upon secretion from golgi. In one embodiment, the protein is made in insect cells by baculovirus expression system.

In one embodiment, engineered recombinant alphavirus glycoproteins (VGPs) are produced using the baculovirus expression system and have comparable targeting specificity to the native virus.

In certain embodiments, proper glycosylation is maintained in the fusion protein which does not elicit an undesirable immune response.

In certain embodiments, the fusion protein is soluble. In certain embodiments, the fusion protein is insoluble.

In certain embodiments, the method disclosed herein is a direct killing of tumor cells. In certain embodiments, the method disclosed herein is an induction of apoptosis which occurs at viral entry and does not require viral replication. In certain embodiments, the glycoproteins on the fusion protein induce apoptosis. In certain embodiments, release of other tumor associated antigens effectuate tumor killing. In certain embodiments, presentation of viral proteins on tumor cell surface induce cytotoxic T cell and/or NK responses.

In certain embodiments, the recombinant expression vector is delivered via certain delivery vehicles. The delivery vehicles may be RNA or DNA based vehicles, lipid based vehicles, cell based vehicles, biodegradable polymer microspheres, liposomes, colloidal gold particles or lipopolysaccharides. Naked DNA may also be delivered by mechanical or electrical techniques such as ballistic transfer using particle bombardment equipment such as a gene gun.

In one embodiment, VGP-TAA fusion protein is generated by recombinant expression vector. In one embodiment, the Sindbis fusion glycoprotein is generated by baculovirus expression in Sf9 insect cells. The baculovirus system is a versatile and powerful eukaryotic vector system using insect cells for recombinant protein expression (10), offering numerous advantages over other expression vector systems. Since baculoviruses can only infect specific invertebrate species, they are nonpathogenic to mammals. Unlike bacterial protein expression, proteins expressed in the baculovirus system are processed, folded, and modified similarly to those produced in a mammalian expression system. Additionally, baculovirus-expressed proteins are easily scaled up to produce large quantities of recombinant protein. Insect cell lines are available that grow well in suspension cultures, allowing the production of recombinant proteins in large-scale bioreactors. Use of the baculovirus system provides another distinct advantage specific for our protein. While both insect and mammalian cells are both capable of making N-linked glycosylations, the specific glycosylation pathway is different. N-glycans produced in insect cells can have either a high-mannose or paucimannosidic structure, both of which have terminal mannose residues (11). N-glycans produced in mammalian cells can have either a high-mannose structure or a complex structure terminating in galactose and sialic acid (11). The gene encoding the VGP is produced through gene synthesis and codon-optimized for insect cell expression. The recombinant fusion protein composed of the ectodomains of the pE2 and E1 Sindbis glycoproteins connected by a flexible linker and linked to a TAA by a second linker (see FIG. 3). In one embodiment, the TAA is NY-ESO-1. In other embodiment, other TAA is inserted to the coding sequence. In certain embodiments, a construct is generated with two or more TAAs in tandem, which could result in a more potent immune response.

In certain embodiments, any type of immune response e.g. T cell mediated and antibody mediated responses can be initiated with epitopes of antigens having various strengths to elicit an immune response. In certain embodiments, the fusion protein successfully elicit an immune response against tumor associated antigen that are known to be too weak using conventional immunization methods. In certain embodiments, the fusion protein as disclosed herein successfully elicit immune response that are 5-10 folds, 10-20 folds, 20-30 folds, 30-50 folds, 50-100 folds, 100-500 folds, 500-1,000 folds greater than conventional immunization methods. Saroja, Laskshmi, and Bhaskaran. Int J Pharm Investig. 2011.

In certain embodiment, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 30, 40, 50 or more TAA are conjugated to the VGP. The E3 component of pE2 acts as a signal peptide for secretion of the protein, assists in the binding of E1 and E2, and is cleaved from the mature protein by furin (7). The mature secreted protein forms a trimer of the heterodimeric complex of E2 and E1, mimicking the trimeric glycoprotein spike observed on the SINV envelope. The second flexible linker allows proper folding of NY-ESO-1 without interfering with the multimerization of E2/E1. In certain embodiment, the TAA contains amino acid residues 1-180 of NY-ESO-1. In other embodiment, the TAA contains amino acid residues 81-180 of NY-ESO-1. In certain embodiment, a His-tag is added to the C-terminus of the protein for purification purposes. The fusion protein is analyzed to determine its multimeric structure by non-denaturing gel and size-exclusion chromatography. The fusion protein is analyzed by ELISA and western blot assays specific. The fusion protein has several antigenic targets (NY-ESO-1, His-tag, and SINV E1 and E2) that could be detected with commercial antibodies. In certain embodiment, the TAA is RGL4. In certain embodiment, the TAA is E6 protein of the human papiloma virus. In certain embodiment, the TAA is E7 protein of the human papiloma virus.

Also disclosed is a cell comprising the nucleic acid construct which encode the fusion protein. Such a recombinant cell can be used as a tool for in vitro research, as a delivery vehicle for the nucleic acid construct or as part of a gene therapy regimen.

Also disclosed is an antibody or binding fragments that immunospecifically bind the fusion protein disclosed herein. In certain embodiments, the antibody is immunoglobulin molecules and active fragments thereof that immunospecifically binds the antigen. The antibodies and binding fragments may be used for immunization of a subject. The antibodies and binding fragments may be used in an assay for detecting the antigen.

5.3 Immunogenic Compositions and Medicaments

Polypeptides of the invention are useful as active ingredients (immunogens) in immunogenic compositions, and such compositions may be useful as vaccines. Vaccines according to the invention may either be prophylactic (i.e. to prevent infection) or therapeutic (i.e. to treat infection), but will typically be prophylactic.

Immunogenic compositions will be pharmaceutically acceptable. They will usually include components in addition to the antigens e.g. they typically include one or more pharmaceutical carrier(s), excipient(s) and/or adjuvant(s). Also disclosed is a vaccine comprising a nucleic acid sequence encoding a fusion protein comprising one or more alpha virus surface membrane glycoprotein operatively linked to one or more tumor associated antigen. The vaccine may thus comprise a nucleic acid construct or comprises a fusion protein as defined above. The vaccine may furthermore be used as a medicament.

The vaccine composition can be formulated according to known methods such as by the admixture of one or more pharmaceutically acceptable carriers, also known as excipients or stabilizers' with the active agent. These excipients may be acceptable for administration to a subject, preferably to vertebrates and more preferably to humans as they are non-toxic to the cell or individual being exposed thereto at the dosages and concentrations employed. In certain embodiments, an acceptable carrier is an aqueous pH buffered solution. Examples of such excipients, carriers and formulation may be found e.g. in Remington's Pharmaceutical Sciences (Maack Publishing Co, Easton, Pa.). Examples of physiologically acceptable carriers include but are not limited to: buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN™, polyethylene glycol (PEG), and PLURONICS™.

To formulate a pharmaceutically acceptable composition suitable for effective administration, such compositions will contain an effective amount of the nucleic acid construct, the nucleic acid construct comprised within a delivery vehicle or the fusion protein as described herein. A carrier may be used as a scaffold by coupling the fusion proteins to improve the induction of an immune response. The carrier protein may be any conventional carrier including any protein suitable for presenting immunogenic determinants. Suitable carriers are typically large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, lipid aggregates (such as oil droplets or liposomes), and inactive virus particles. Such carriers are well known to those of ordinary skill in the art. Additionally, these carriers may function as immunostimulating agents (“adjuvants”). Immunization of the animal may be carried out with adjuvants and/or pharmaceutical carriers. Conventional carrier proteins include, but are not limited to, keyhole limpet hemocyanin, serum proteins such as transferrin, bovine serum albumin, or human serum albumin, an ovalbumin, immunoglobulins, or hormones, such as insulin. The carrier may be present together with an adjuvant. Vaccine compositions are useful for prophylactic and therapeutic use, including stimulating an immune response in a subject. The vaccine composition disclosed herein does not induce any systemic or local toxicity reactions or any other side effects.

Adjuvants may be included in the vaccine composition to enhance the specific immune response. Thus, it is particularly important to identify an adjuvant that when combined with the antigen(s)/nucleic acid constructs and/or delivery vehicles (any of which may also be referred to as immunogenic determinant), results in a vaccine composition capable of inducing a strong specific immunological response. The immunogenic determinant may also be mixed with two or more different adjuvants prior to immunization. A large number of adjuvants have been described and used for the generation of antibodies in laboratory animals, such as mouse, rats and rabbits. In such setting the tolerance of side effect is rather high as the main aim is to obtain a strong antibody response. For use and for approval for use in pharmaceuticals, and especially for use in humans it is required that the components of the vaccine composition, including the adjuvant, are well characterized. It is further required that the composition has minimal risk of any adverse effects. In one embodiment, a vaccine composition comprises an adjuvant. In a preferred embodiment the vaccine composition is suitable for administration to a mammal, and most preferably to a human subject. The choice of adjuvant may further be selected by its ability to stimulate the type of immune response desired, B-cell or/and T-cell activation and the vaccine composition may be formulated to optimize distribution and presentation to the relevant lymphatic tissues.

Lipopolysaccharide and its various derivatives, including lipid A, have been found to be powerful adjuvants in combination with liposomes or other lipid emulsions. Freund's Complete Adjuvant is the standard in most experimental studies. Mineral oil may be added to the immunogenic composition in order to protect the antigen from rapid catabolism. Many other types of materials can be used as adjuvants in immunogenic compositions include plant products such as saponin, animal products such as chitin and numerous synthetic chemicals.

Immunogenic compositions may also contain diluents such as buffers, antioxidants such as ascorbic acid, low molecular weight (less than about 10 residues) polypeptides, proteins, amino acids, carbohydrates including glucose, sucrose or dextrins, chelating agents such as EDTA, glutathione and other stabilizers and excipients. Neutral buffered saline or saline mixed with non-specific serum albumin are exemplary appropriate diluents.

The pH of a composition will generally be between 5.0 and 8.1, and more typically between 6.0 and 8.0 e.g. 6.5 and 7.5, or between 7.0 and 7.8.

The composition is preferably sterile. The composition is preferably non-pyrogenic e.g. containing <1 EU (endotoxin unit, a standard measure) per dose, and preferably <0.1 EU per dose. The composition is preferably gluten free.

5.4 Dosage

Vaccine compositions disclosed herein are typically administered to a subject in an amount sufficient to provide a benefit to the subject. This amount is defined as a “therapeutically effective amount.” The therapeutically effective amount will be determined by the efficacy or potency of the particular composition, the duration or frequency of administration, and the size and condition of the subject, including that subject's particular treatment response. Additionally, the route of administration should be considered when determining the therapeutically effective amount. It is anticipated that the therapeutically effective amount of a vaccine composition will range from about 0.1 μg/kg to 1 mg/kg of total nucleic acid. Suitable doses include from about 5 μg/kg-500 mg/kg of total DNA, 10 μg/kg-250 μg/kg of total DNA, or 10 μg/kg-170 μg/kg of total DNA. In one embodiment, a human subject (18-50 years of age, 45-75 kg) is administered 1.2 mg-7.2 mg of DNA. “Total DNA” and “total nucleic acid” refers to a pool of nucleic acids encoding distinct immunogenic molecules. For example, a dose of 50 mg of total DNA encoding 5 different immunogenic molecules can have 1 mg of each molecule. The vaccines may be administered multiple times, such as between about 2-6 times. In an exemplary method, 100 μg of a DNA composition is administered to a human subject at 0, 4, and 12 weeks (100 μg per administration). The therapeutically effective amount of a vaccine composition will range from about 0.1 μg/kg to 1 mg/kg of fusion protein. Suitable doses include from about 5 μg/kg-500 mg/kg of fusion protein, 10 μg/kg-250 μg/kg of fusion protein, or 10 μg/kg-170 μg/kg of fusion protein. In one embodiment, a human subject (18-50 years of age, 45-75 kg) is administered 1.2 mg-7.2 mg of fusion protein. Human vaccines are typically administered in a dosage volume of about 0.5 ml, although a half dose (i.e. about 0.25 ml) may be administered to children.

The treatments of the present application may include various ‘unit doses.’ A unit dose is defined as containing a predetermined-quantity of the therapeutic composition of the present application. The quantity to be administered, and the particular route and formulation, are within the skill of those in the clinical arts. A unit dose need not be administered as a single injection but may comprise continuous infusion over a set period of time. A unit dose may contain at least 0.01, 0.05, 0.1, 0.5, 1.0, 2.5, 5.0, 10.0, 15.0, 25.0 or 50.0 mg of the active ingredient. Optionally, a unit dose contains less than 0.01, 0.05, 0.1, 0.5, 1.0, 2.5, 5.0, 10.0, 15.0, 25.0 or 50.0 mg of the active ingredient. In at least one embodiment, a unit dose contains from about 0.001 mg to about 50 mg of the active ingredient. In one or more embodiments, a unit dose contains from about 1 mg to about 10 mg of active ingredient.

5.5 Administration

Vaccine compositions may be administered to a subject in therapeutically effective amounts. The effective amount may vary according to a variety of factors such as the subject's condition, weight, sex and age. Other factors include the mode of administration. The pharmaceutical or veterinary compositions may be provided to the individual by a variety of routes such as subcutaneous, topical, oral and intramuscular. Administration of pharmaceutical compositions is accomplished orally or parenterally. Methods of parenteral delivery include topical, intra-arterial (directly to the tissue), intramuscular, subcutaneous, intramedullary, intrathecal, intraventricular, intravenous, intraperitoneal, or intranasal administration. Also provided are suitable topical, oral, systemic and parenteral pharmaceutical formulations for use in the methods of prophylaxis and treatment with the vaccine composition.

For example, the vaccine compositions can be administered in such oral dosage forms as tablets, capsules (each including timed release and sustained release formulations), pills, powders, granules, elixirs, tinctures, solutions, suspensions, syrups and emulsions, or by injection. Likewise, they may also be administered in intravenous (both bolus and infusion), intraperitoneal, subcutaneous, topical with or without occlusion, or intramuscular form, all using forms well known to those of ordinary skill in the pharmaceutical arts. An effective but non-toxic amount of the vaccine, comprising any of the herein described compounds can be employed as a prophylactic or therapeutic agent. Also any and all conventional dosage forms that are known in the art to be appropriate for formulating injectable immunogenic peptide composition are encompassed, such as lyophilized forms and solutions, suspensions or emulsion forms containing, if required, conventional pharmaceutically acceptable carriers, diluents, preservatives, adjuvants, buffer components, etc.

Preferred modes of administration of the vaccine composition include, but are not limited to systemic administration, such as intravenous or subcutaneous administration, intradermal administration, intramuscular administration, intranasal administration, oral administration, rectal administration, vaginal administration, pulmonary administration and generally any form of mucosal administration.

A vaccine described herein can be administered once, two, three, four, five or more times. Administering the vaccine more than once has the effect of boosting the resulting immune response. The vaccine can further be boosted by administering the vaccine in a form different from the previous administration. The booster shot is either a homologous or a heterologous booster shot. A homologous booster shot is a where the first and subsequent vaccinations comprise the same constructs, fusion proteins, and more specifically the same delivery vehicle. A heterologous booster shot is where identical constructs or fusion proteins are comprised within different vectors.

A preferred recipient of the vaccine is a mammal and the mammal is in a more preferred embodiment, the subject is selected from the group of: cows, pigs, horses, sheep, goats, llamas, mice, rats, monkeys, dogs, cats and humans.

In one embodiment, the vaccine composition further comprises a second active ingredient. The second active ingredient is antibiotics, chemotherapeutics, anti-allergenics, cytokines, complement factors and co-stimulatory molecules of the immune system.

5.6 Methods of Treatment and Prevention

Also disclosed is a method for inducing an immune response in a subject, comprising administering to the subject, a vaccine described herein. The immune response includes the following types of responses: an MHC-I dependent response, an MHC-I and/or MHC-II dependent response, a T-cell dependent response, a CD4 T ell dependent response, a CD4⁺ T cell independent response, a CD8⁺ T-cell dependent response and a B cell dependent immune response. The method is used for genetic immunization of an animal, or to treat a clinical condition in a subject in need thereof.

As discussed herein, ‘treatment’ includes both therapeutic treatment and prophylactic or preventative treatment, wherein the object is to prevent or slow down the targeted pathologic condition or disorder. Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented. The terms ‘therapy’, ‘therapeutic’, ‘treatment’ or ‘treating’ include the ability or action of reducing, alleviating or inhibiting or eliminating the symptoms or progress of a disease. Desirable effects of treatment include preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. In some embodiments, methods and compositions of the present application are used to delay development of a disease or disorder or to slow the progression of a disease or disorder.

Treatment in accordance with the present application can include a method of treating a cancer or other neoplastic disorder which comprises administering to a patient in need of treatment a peptide, nucleic acid, antibody composition of the present application. In at least one embodiment, the treatment further comprises administering to said patient a chemotherapeutic drug, such as a drug in prodrug form. The two components may be administered together, for example in the form of a combined pill, or separately. Administration may also be sequential or simultaneous. ‘Sequential’ administration indicates that the components are administered at different times or time points, which may nonetheless be overlapping. Simultaneous administration indicates that the components are administered at the same time.

An effective amount, or preferably a therapeutically effective amount of the treatment of the present application is administered. An “effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic or prophylactic result. The effective amount may vary according to the drug or prodrug with which the treatment is co-administered. A “therapeutically effective amount” of a treatment of the present application may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the protein, to elicit a desired therapeutic result. A therapeutically effective amount encompasses an amount in which any toxic or detrimental effects of the protein are outweighed by the therapeutically beneficial effects. A therapeutically effective amount also encompasses an amount sufficient to confer benefit, e.g., clinical benefit.

The invention also provides a method for raising an immune response in a mammal comprising the step of administering an effective amount of a composition of the invention. The immune response is preferably protective and preferably involves antibodies and/or cell-mediated immunity. The method may raise a booster response.

The invention also provides a polypeptide of the invention for use as a medicament e.g. for use in raising an immune response in a mammal.

The invention also provides the use of a polypeptide of the invention in the manufacture of a medicament for raising an immune response in a mammal.

The invention also provides a delivery device pre-filled with an immunogenic composition of the invention.

By raising an immune response in the mammal by these uses and methods, the mammal can be protected against latent viral infections including HIV, Shingles and herpes.

The mammal is preferably a human, but may be e.g. a cow, a pig, a chicken, a cat or a dog, as E. coli disease is also problematic in these species. Where the vaccine is for prophylactic use, the human is preferably a child (e.g. a toddler or infant) or a teenager; where the vaccine is for therapeutic use, the human is preferably a teenager or an adult. A vaccine intended for children may also be administered to adults e.g. to assess safety, dosage, immunogenicity, etc. Vaccines of the invention may be used to treat both children and adults. Thus a human patient may be less than 1 year old, 1-5 years old, 5-15 years old, 15-55 years old, or at least 55 years old. Preferred patients for receiving the vaccines are the elderly (e.g. ≥50 years old, ≥60 years old, and preferably ≥65 years), the young (e.g. ≥5 years old), hospitalised patients, healthcare workers, armed service and military personnel, pregnant women, the chronically ill, or immunodeficient patients. The vaccines are not suitable solely for these groups, however, and may be used more generally in a population.

One way of checking efficacy of therapeutic treatment involves monitoring E. coli infection after administration of the compositions of the invention. One way of checking efficacy of prophylactic treatment involves monitoring immune responses, systemically (such as monitoring the level of IgG1 and IgG2a production) and/or mucosally (such as monitoring the level of IgA production), against the antigens in the compositions of the invention after administration of the composition. Typically, antigen-specific serum antibody responses are determined post-immunisation but pre-challenge whereas antigen-specific mucosal antibody responses are determined post-immunisation and post-challenge.

Another way of assessing the immunogenicity of the compositions of the present invention is to express the proteins recombinantly for screening patient sera or mucosal secretions by immunoblot and/or microarrays. A positive reaction between the protein and the patient sample indicates that the patient has mounted an immune response to the protein in question. This method may also be used to identify immunodominant antigens and/or epitopes within antigens.

Also disclosed is a method to stimulate growth of Human T Cells by treating with an alpha virus surface membrane glycoprotein

Also disclosed is a method to excite Human hemopoietic cells by treating with an alpha virus surface membrane glycoprotein (including T Cells, NK cells, B Cells, dendritic cells, regulatory T Cells, macrophages, erythrocytes and all others).

Also disclosed is a method to release T Cells from anergy by treating with an alpha virus surface membrane glycoprotein.

Also disclosed is a method to overcome Breakpoint Inhibition of T Cells by treating with an alpha virus surface membrane glycoprotein.

Also disclosed is a method to treat cancer by treating with an alpha virus surface membrane glycoprotein.

5.6.1. Combination Therapy

In certain embodiments, the fusion protein can be used in combination therapy with at least one other therapeutic agent. The fusion protein and the therapeutic agent can act additively or, more preferably, synergistically. In a preferred embodiment, a composition comprising a fusion protein is administered concurrently with the administration of another therapeutic agent, which can be part of the same composition as the fusion protein or different composition. In another embodiment, a composition comprising a fusion protein is administered prior or subsequent to administration of another therapeutic agent. As many of the disorders for which the fusion protein are useful in treating are chronic disorders, in one embodiment combination therapy involves alternating between administering a composition comprising a fusion protein and a composition comprising another therapeutic agent, e.g., to minimize the toxicity associated with a particular drug. The duration of administration of each drug or therapeutic agent can be, e.g., one month, three months, six months, or a year. In certain embodiments, when a fusion protein is administered concurrently with another therapeutic agent that potentially produces adverse side effects including but not limited to toxicity, the therapeutic agent can advantageously be administered at a dose that falls below the threshold at which the adverse side is elicited.

In certain embodiment, the fusion protein is administered with a check point therapy or chemotherapy. In certain embodiment, the fusion protein is administered with antibodies to CTLA4, PD1 or PDL1.

The present fusion protein can be administered together with treatment with irradiation or one or more chemotherapeutic agents. For irradiation treatment, the irradiation can be gamma rays or X-rays. For a general overview of radiation therapy, see Hellman, Chapter 12: Principles of Radiation Therapy Cancer, in: Principles and Practice of Oncology, DeVita et al., eds., 2.nd. Ed., J.B. Lippencott Company, Philadelphia. Useful chemotherapeutic agents include methotrexate, taxol, mercaptopurine, thioguanine, hydroxyurea, cytarabine, cyclophosphamide, ifosfamide, nitrosoureas, cisplatin, carboplatin, mitomycin, dacarbazine, procarbizine, etoposides, campathecins, bleomycin, doxorubicin, idarubicin, daunorubicin, dactinomycin, plicamycin, mitoxantrone, asparaginase, vinblastine, vincristine, vinorelbine, paclitaxel, and docetaxel. In a specific embodiment, a composition comprising the fusion protein further comprises one or more chemotherapeutic agents and/or is administered concurrently with radiation therapy. In another specific embodiment, chemotherapy or radiation therapy is administered prior or subsequent to administration of a present composition, preferably at least an hour, five hours, 12 hours, a day, a week, a month, more preferably several months (e.g., up to three months), subsequent to administration of a composition comprising the fusion protein.

Any therapy (e.g., therapeutic or prophylactic agent) which is useful, has been used, or is currently being used for the prevention, treatment, and/or management of a disorder, e.g., cancer, can be used in compositions and methods of the invention. Therapies (e.g., therapeutic or prophylactic agents) include, but are not limited to, peptides, polypeptides, conjugates, nucleic acid molecules, small molecules, mimetic agents, synthetic drugs, inorganic molecules, and organic molecules. Non-limiting examples of cancer therapies include chemotherapies, radiation therapies, hormonal therapies, and/or biological therapies/immunotherapies and surgery. In certain embodiments, a prophylactically and/or therapeutically effective regimen of the invention comprises the administration of a combination of therapies.

Examples of cancer therapies include, but not limited to: acivicin; aclarubicin; acodazole hydrochloride; acronine; adozelesin; aldesleukin; altretamine; ambomycin; ametantrone acetate; aminoglutethimide; amsacrine; anastrozole; anthramycin; asparaginase; asperlin; azacitidine; azetepa; azotomycin; batimastat; benzodepa; bicalutamide; bisantrene hydrochloride; bisnafide dimesylate; bisphosphonates (e.g., pamidronate (Aredria), sodium clondronate (Bonefos), zoledronic acid (Zometa), alendronate (Fosamax), etidronate, ibandornate, cimadronate, risedromate, and tiludromate); bizelesin; bleomycin sulfate; brequinar sodium; bropirimine; busulfan; cactinomycin; calusterone; caracemide; carbetimer; carboplatin; carmustine; carubicin hydrochloride; carzelesin; cedefingol; chlorambucil; cirolemycin; cisplatin; cladribine; crisnatol mesylate; cyclophosphamide; cytarabine; dacarbazine; dactinomycin; daunorubicin hydrochloride; decitabine; dexormaplatin; dezaguanine; dezaguanine mesylate; diaziquone; docetaxel; doxorubicin; doxorubicin hydrochloride; droloxifene; droloxifene citrate; dromostanolone propionate; duazomycin; edatrexate; eflornithine hydrochloride; EphA2 inhibitors; elsamitrucin; enloplatin; enpromate; epipropidine; epirubicin hydrochloride; erbulozole; esorubicin hydrochloride; estramustine; estramustine phosphate sodium; etanidazole; etoposide; etoposide phosphate; etoprine; fadrozole hydrochloride; fazarabine; fenretinide; floxuridine; fludarabine phosphate; fluorouracil; fluorocitabine; fosquidone; fostriecin sodium; gemcitabine; gemcitabine hydrochloride; hydroxyurea; idarubicin hydrochloride; ifosfamide; ilmofosine; interleukin II (including recombinant interleukin II, or rIL2), interferon alpha-2a; interferon alpha-2b; interferon alpha-n1; interferon alpha-n3; interferon beta-I a; interferon gamma-I b; iproplatin; irinotecan hydrochloride; lanreotide acetate; letrozole; leuprolide acetate; liarozole hydrochloride; lometrexol sodium; lomustine; losoxantrone hydrochloride; masoprocol; maytansine; mechlorethamine hydrochloride; anti-CD2 antibodies; megestrol acetate; melengestrol acetate; melphalan; menogaril; mercaptopurine; methotrexate; methotrexate sodium; metoprine; meturedepa; mitindomide; mitocarcin; mitocromin; mitogillin; mitomalcin; mitomycin; mitosper; mitotane; mitoxantrone hydrochloride; mycophenolic acid; nocodazole; nogalamycin; ormaplatin; oxisuran; paclitaxel; pegaspargase; peliomycin; pentamustine; peplomycin sulfate; perfosfamide; pipobroman; piposulfan; piroxantrone hydrochloride; plicamycin; plomestane; porfimer sodium; porfiromycin; prednimustine; procarbazine hydrochloride; puromycin; puromycin hydrochloride; pyrazofurin; riboprine; rogletimide; safingol; safingol hydrochloride; semustine; simtrazene; sparfosate sodium; sparsomycin; spirogermanium hydrochloride; spiromustine; spiroplatin; streptonigrin; streptozocin; sulofenur; talisomycin; tecogalan sodium; tegafur; teloxantrone hydrochloride; temoporfin; teniposide; teroxirone; testolactone; thiamiprine; thioguanine; thiotepa; tiazofurin; tirapazamine; toremifene citrate; trestolone acetate; triciribine phosphate; trimetrexate; trimetrexate glucuronate; triptorelin; tubulozole hydrochloride; uracil mustard; uredepa; vapreotide; verteporfin; vinblastine sulfate; vincristine sulfate; vindesine; vindesine sulfate; vinepidine sulfate; vinglycinate sulfate; vinleurosine sulfate; vinorelbine tartrate; vinrosidine sulfate; vinzolidine sulfate; vorozole; zeniplatin; zinostatin; zorubicin hydrochloride.

Other examples of cancer therapies include, but are not limited to: 20-epi-1,25 dihydroxyvitamin D3; 5-ethynyluracil; abiraterone; aclarubicin; acylfulvene; adecypenol; adozelesin; aldesleukin; ALL-TK antagonists; altretamine; ambamustine; amidox; amifostine; aminolevulinic acid; amrubicin; amsacrine; anagrelide; anastrozole; andrographolide; angiogenesis inhibitors; antagonist D; antagonist G; antarelix; anti-dorsalizing morphogenetic protein-1; antiandrogen, prostatic carcinoma; antiestrogen; antineoplaston; antisense oligonucleotides; aphidicolin glycinate; apoptosis gene modulators; apoptosis regulators; apurinic acid; ara-CDP-DL-PTBA; arginine deaminase; asulacrine; atamestane; atrimustine; axinastatin 1; axinastatin 2; axinastatin 3; azasetron; azatoxin; azatyrosine; baccatin III derivatives; balanol; batimastat; Bcl-2 inhibitors; Bcl-2 family inhibitors, including ABT-737; BCR/ABL antagonists; benzochlorins; benzoylstaurosporine; beta lactam derivatives; beta-alethine; betaclamycin B; betulinic acid; bFGF inhibitor; bicalutamide; bisantrene; bisaziridinylspermine; bisnafide; bistratene A; bizelesin; breflate; bropirimine; budotitane; buthionine sulfoximine; calcipotriol; calphostin C; camptothecin derivatives; canarypox IL-2; capecitabine; carboxamide-amino-triazole; carboxyamidotriazole; CaRest M3; CARN 700; cartilage derived inhibitor; carzelesin; casein kinase inhibitors (ICOS); castanospermine; cecropin B; cetrorelix; chlorins; chloroquinoxaline sulfonamide; cicaprost; cis-porphyrin; cladribine; clomifene analogues; clotrimazole; collismycin A; collismycin B; combretastatin A4; combretastatin analogue; conagenin; crambescidin 816; crisnatol; cryptophycin 8; cryptophycin A derivatives; curacin A; cyclopentanthraquinones; cycloplatam; cypemycin; cytarabine ocfosfate; cytolytic factor; cytostatin; dacliximab; decitabine; dehydrodidemnin B; deslorelin; dexamethasone; dexifosfamide; dexrazoxane; dexverapamil; diaziquone; didemnin B; didox; diethylnorspermine; dihydro-5-azacytidine; dihydrotaxol, dioxamycin; diphenyl spiromustine; docetaxel; docosanol; dolasetron; doxifluridine; droloxifene; dronabinol; duocarmycin SA; ebselen; ecomustine; edelfosine; edrecolomab; eflornithine; elemene; emitefur; epirubicin; epristeride; estramustine analogue; estrogen agonists; estrogen antagonists; etanidazole; etoposide phosphate; exemestane; fadrozole; fazarabine; fenretinide; filgrastim; finasteride; flavopiridol; flezelastine; fluasterone; fludarabine; fluorodaunorunicin hydrochloride; forfenimex; formestane; fostriecin; fotemustine; gadolinium texaphyrin; gallium nitrate; galocitabine; ganirelix; gelatinase inhibitors; gemcitabine; glutathione inhibitors; HMG CoA reductase inhibitors (e.g., atorvastatin, cerivastatin, fluvastatin, lescol, lupitor, lovastatin, rosuvastatin, and simvastatin); hepsulfam; heregulin; hexamethylene bisacetamide; hypericin; ibandronic acid; idarubicin; idoxifene; idramantone; ilmofosine; ilomastat; imidazoacridones; imiquimod; immunostimulant peptides; insulin-like growth factor-1 receptor inhibitor; interferon agonists; interferons; interleukins; iobenguane; iododoxorubicin; ipomeanol, 4-iroplact; irsogladine; isobengazole; isohomohalicondrin B; itasetron; jasplakinolide; kahalalide F; lamellarin-N triacetate; lanreotide; leinamycin; lenograstim; lentinan sulfate; leptolstatin; letrozole; leukemia inhibiting factor; leukocyte alpha interferon; leuprolide+estrogen+progesterone; leuprorelin; levamisole; LFA-3TIP; liarozole; linear polyamine analogue; lipophilic disaccharide peptide; lipophilic platinum compounds; lissoclinamide 7; lobaplatin; lombricine; lometrexol; lonidamine; losoxantrone; lovastatin; loxoribine; lurtotecan; lutetium texaphyrin; lysofylline; lytic peptides; maitansine; mannostatin A; marimastat; masoprocol; maspin; matrilysin inhibitors; matrix metalloproteinase inhibitors; menogaril; merbarone; meterelin; methioninase; metoclopramide; MIF inhibitor; mifepristone; miltefosine; mirimostim; mismatched double stranded RNA; mitoguazone; mitolactol; mitomycin analogues; mitonafide; mitotoxin fibroblast growth factor-saporin; mitoxantrone; mofarotene; molgramostim; monoclonal antibody, human chorionic gonadotrophin; monophosphoryl lipid A+myobacterium cell wall sk; mopidamol; multiple drug resistance gene inhibitor; multiple tumor suppressor 1-based therapy; mustard anticancer agent; mycaperoxide B; mycobacterial cell wall extract; myriaporone; N-acetyldinaline; N-substituted benzamides; nafarelin; nagrestip; naloxone+pentazocine; napavin; naphterpin; nartograstim; nedaplatin; nemorubicin; neridronic acid; neutral endopeptidase; nilutamide; nisamycin; nitric oxide modulators; nitroxide antioxidant; nitrullyn; O6-benzylguanine; octreotide; okicenone; oligonucleotides; onapristone; ondansetron; ondansetron; oracin; oral cytokine inducer; ormaplatin; osaterone; oxaliplatin; oxaunomycin; paclitaxel; paclitaxel analogues; paclitaxel derivatives; palauamine; palmitoylrhizoxin; pamidronic acid; panaxytriol; panomifene; parabactin; pazelliptine; pegaspargase; peldesine; pentosan polysulfate sodium; pentostatin; pentrozole; perflubron; perfosfamide; perillyl alcohol; phenazinomycin; phenylacetate; phosphatase inhibitors; picibanil; pilocarpine hydrochloride; pirarubicin; piritrexim; placetin A; placetin B; plasminogen activator inhibitor; platinum complex; platinum compounds; platinum-triamine complex; porfimer sodium; porfiromycin; prednisone; propyl bis-acridone; prostaglandin J2; proteasome inhibitors; protein A-based immune modulator; protein kinase C inhibitor; protein kinase C inhibitors, microalgal; protein tyrosine phosphatase inhibitors; purine nucleoside phosphorylase inhibitors; purpurins; pyrazoloacridine; pyridoxylated hemoglobin polyoxyethylene conjugate; raf antagonists; raltitrexed; ramosetron; ras farnesyl protein transferase inhibitors; ras inhibitors; ras-GAP inhibitor; retelliptine demethylated; rhenium Re 186 etidronate; rhizoxin; ribozymes; RH retinamide; rogletimide; rohitukine; romurtide; roquinimex; rubiginone B1; ruboxyl; safingol; saintopin; SarCNU; sarcophytol A; sargramostim; Sdi 1 mimetics; semustine; senescence derived inhibitor 1; sense oligonucleotides; signal transduction inhibitors; signal transduction modulators; single chain antigen binding protein; sizofuran; sobuzoxane; sodium borocaptate; sodium phenylacetate; solverol; somatomedin binding protein; sonermin; sparfosic acid; spicamycin D; spiromustine; splenopentin; spongistatin 1; squalamine; stem cell inhibitor; stem-cell division inhibitors; stipiamide; stromelysin inhibitors; sulfinosine; superactive vasoactive intestinal peptide antagonist; suradista; suramin; swainsonine; synthetic glycosaminoglycans; tallimustine; 5-fluorouracil; leucovorin; tamoxifen methiodide; tauromustine; tazarotene; tecogalan sodium; tegafur; tellurapyrylium; telomerase inhibitors; temoporfin; temozolomide; teniposide; tetrachlorodecaoxide; tetrazomine; thaliblastine; thiocoraline; thrombopoietin; thrombopoietin mimetic; thymalfasin; thymopoietin receptor agonist; thymotrinan; thyroid stimulating hormone; tin ethyl etiopurpurin; tirapazamine; titanocene bichloride; topsentin; toremifene; totipotent stem cell factor; translation inhibitors; tretinoin; triacetyluridine; triciribine; trimetrexate; triptorelin; tropisetron; turosteride; tyrosine kinase inhibitors; tyrphostins; UBC inhibitors; ubenimex; urogenital sinus-derived growth inhibitory factor; urokinase receptor antagonists; vapreotide; variolin B; vector system, erythrocyte gene therapy; thalidomide; velaresol; veramine; verdins; verteporfin; vinorelbine; vinxaltine; vorozole; zanoterone; zeniplatin; zilascorb; and zinostatin stimalamer.

In some embodiments, the therapy(ies) used in combination with the fusion protein is an immunomodulatory agent. Non-limiting examples of immunomodulatory agents include proteinaceous agents such as cytokines, peptide mimetics, and antibodies (e.g., human, humanized, chimeric, monoclonal, polyclonal, Fvs, ScFvs, Fab or F(ab)2 fragments or epitope binding fragments), nucleic acid molecules (e.g., antisense nucleic acid molecules and triple helices), small molecules, organic compounds, and inorganic compounds. In particular, immunomodulatory agents include, but are not limited to, methotrexate, leflunomide, cyclophosphamide, cytoxan, Immuran, cyclosporine A, minocycline, azathioprine, antibiotics (e.g., FK506 (tacrolimus)), methylprednisolone (MP), corticosteroids, steroids, mycophenolate mofetil, rapamycin (sirolimus), mizoribine, deoxyspergualin, brequinar, malononitriloamindes (e.g., leflunamide). In one embodiment, the immunomodulatory agent is a chemotherapeutic agent. In an alternative embodiment, the immunomodulatory agent is an immunomodulatory agent other than a chemotherapeutic agent. In some embodiments, the therapy(ies) used in accordance with the invention is not an immunomodulatory agent.

In some embodiments, the therapy(ies) used in combination with fusion protein is an anti-angiogenic agent. Non-limiting examples of anti-angiogenic agents include proteins, polypeptides, peptides, conjugates, antibodies (e.g., human, humanized, chimeric, monoclonal, polyclonal, Fvs, ScFvs, Fab fragments, F(ab)2 fragments, and antigen-binding fragments thereof) such as antibodies that bind to TNF-alpha, nucleic acid molecules (e.g., antisense molecules or triple helices), organic molecules, inorganic molecules, and small molecules that reduce or inhibit angiogenesis. Other examples of anti-angiogenic agents can be found, e.g., in U.S. Publ'n No. 2005/0002934 A1 at paragraphs 277-282, which is incorporated by reference in its entirety. In other embodiments, the therapy(ies) used in accordance with the invention is not an anti-angiogenic agent.

In some embodiments, the therapy(ies) used in combination with the fusion protein is an inflammatory agent. Non-limiting examples of anti-inflammatory agents include any anti-inflammatory agent, including agents useful in therapies for inflammatory disorders, well-known to one of skill in the art. Non-limiting examples of anti-inflammatory agents include non-steroidal anti-inflammatory drugs (NSAIDs), steroidal anti-inflammatory drugs, anticholinergics (e.g., atropine sulfate, atropine methylnitrate, and ipratropium bromide (ATROVENT™)), β2-agonists (e.g., abuterol (VENTOLIN™ and PROVENTIL™), bitolterol (TORNALATE™), levalbuterol (XOPONEX™), metaproterenol (ALUPENT™), pirbuterol (MAXAIR™), terbutlaine (BRETHAIRE™ and BRETHINE™), albuterol (PROVENTIL™, REPETABS™, and VOLMAX™), formoterol (FORADIL AEROLIZER™), and salmeterol (SEREVENT™ and SEREVENT DISKUS™)), and methylxanthines (e.g., theophylline (UNIPHYL™, THEO-DUR™, SLO-BID™, AND TEHO-42™)). Examples of NSAIDs include, but are not limited to, aspirin, ibuprofen, celecoxib (CELEBREX™), diclofenac (VOLTAREN™), etodolac (LODINE™), fenoprofen (NALFON™), indomethacin (INDOCIN™), ketoralac (TORADOL™), oxaprozin (DAYPRO™), nabumentone (RELAFEN™), sulindac (CLINORIL™), tolmentin (TOLECTIN™), rofecoxib (VIOXX™), naproxen (ALEVE™, NAPROSYN™), ketoprofen (ACTRON™) and nabumetone (RELAFEN™). Such NSAIDs function by inhibiting a cyclooxygenase enzyme (e.g., COX-1 and/or COX-2). Examples of steroidal anti-inflammatory drugs include, but are not limited to, glucocorticoids, dexamethasone (DECADRON™), corticosteroids (e.g., methylprednisolone (MEDROL™)), cortisone, hydrocortisone, prednisone (PREDNISONE™ and DELTASONE™), prednisolone (PRELONE™ and PEDIAPRED™), triamcinolone, azulfidine, and inhibitors of eicosanoids (e.g., prostaglandins, thromboxanes, and leukotrienes. In other embodiments, the therapy(ies) used in accordance with the invention is not an anti-inflammatory agent.

In certain embodiments, the therapy(ies) used is an alkylating agent, a nitrosourea, an antimetabolite, and anthracyclin, a topoisomerase II inhibitor, or a mitotic inhibitor. Alkylating agents include, but are not limited to, busulfan, cisplatin, carboplatin, chlorambucil, cyclophosphamide, ifosfamide, decarbazine, mechlorethamine, melphalan, and themozolomide. Nitrosoureas include, but are not limited to carmustine (BCNU) and lomustine (CCNU). Antimetabolites include but are not limited to 5-fluorouracil, capecitabine, methotrexate, gemcitabine, cytarabine, and fludarabine. Anthracyclines include but are not limited to daunorubicin, doxorubicin, epirubicin, idarubicin, and mitoxantrone. Topoisomerase II inhibitors include, but are not limited to, topotecan, irinotecan, etoposide (VP-16), and teniposide. Mitotic inhibitors include, but are not limited to taxanes (paclitaxel, docetaxel), and the vinca alkaloids (vinblastine, vincristine, and vinorelbine).

In some embodiments, the fusion protein is used in combination with radiation therapy comprising the use of x-rays, gamma rays and other sources of radiation to destroy cancer stem cells and/or cancer cells. In specific embodiments, the radiation therapy is administered as external beam radiation or teletherapy, wherein the radiation is directed from a remote source. In other embodiments, the radiation therapy is administered as internal therapy or brachytherapy wherein a radioactive source is placed inside the body close to cancer stem cells, cancer cells and/or a tumor mass.

5.7. Types of Cancer

Any type of cancer can be prevented, treated, and/or managed in accordance with the invention. Non-limiting examples of cancers that can be prevented, treated, and/or managed in accordance with the invention include: leukemias, such as but not limited to, acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemias, such as, myeloblastic, promyelocytic, myelomonocytic, monocytic, and erythroleukemia leukemias and myelodysplastic syndrome; chronic leukemias, such as but not limited to, chronic myelocytic (granulocytic) leukemia, chronic lymphocytic leukemia, hairy cell leukemia; polycythemia vera; lymphomas such as but not limited to Hodgkin's disease, non-Hodgkin's disease; multiple myelomas such as but not limited to smoldering multiple myeloma, nonsecretory myeloma, osteosclerotic myeloma, plasma cell leukemia, solitary plasmacytoma and extramedullary plasmacytoma; Waldenstrom's macroglobulinemia; monoclonal gammopathy of undetermined significance; benign monoclonal gammopathy; heavy chain disease; dendritic cell cancer, including plasmacytoid dendritic cell cancer, NK blastic lymphoma (also known as cutaneous NK/T-cell lymphoma and agranular (CD4+/CD56+) dermatologic neoplasms); basophilic leukemia; bone and connective tissue sarcomas such as but not limited to bone sarcoma, osteosarcoma, chondrosarcoma, Ewing's sarcoma, malignant giant cell tumor, fibrosarcoma of bone, chordoma, periosteal sarcoma, soft-tissue sarcomas, angiosarcoma (hemangiosarcoma), fibrosarcoma, Kaposi's sarcoma, leiomyosarcoma, liposarcoma, lymphangiosarcoma, neurilemmoma, rhabdomyosarcoma, synovial sarcoma; brain tumors such as but not limited to, glioma, astrocytoma, brain stem glioma, ependymoma, oligodendroglioma, nonglial tumor, acoustic neurinoma, craniopharyngioma, medulloblastoma, meningioma, pineocytoma, pineoblastoma, primary brain lymphoma; breast cancer including but not limited to ductal carcinoma, adenocarcinoma, lobular (small cell) carcinoma, intraductal carcinoma, medullary breast cancer, mucinous breast cancer, tubular breast cancer, papillary breast cancer, Paget's disease, and inflammatory breast cancer; adrenal cancer such as but not limited to pheochromocytom and adrenocortical carcinoma; thyroid cancer such as but not limited to papillary or follicular thyroid cancer, medullary thyroid cancer and anaplastic thyroid cancer; pancreatic cancer such as but not limited to, insulinoma, gastrinoma, glucagonoma, vipoma, somatostatin-secreting tumor, and carcinoid or islet cell tumor; pituitary cancers such as but limited to Cushing's disease, prolactin-secreting tumor, acromegaly, and diabetes insipius; eye cancers such as but not limited to ocular melanoma such as iris melanoma, choroidal melanoma, and cilliary body melanoma, and retinoblastoma; vaginal cancers such as squamous cell carcinoma, adenocarcinoma, and melanoma; vulvar cancer such as squamous cell carcinoma, melanoma, adenocarcinoma, basal cell carcinoma, sarcoma, and Paget's disease; cervical cancers such as but not limited to, squamous cell carcinoma, and adenocarcinoma; uterine cancers such as but not limited to endometrial carcinoma and uterine sarcoma; ovarian cancers such as but not limited to, ovarian epithelial carcinoma, borderline tumor, germ cell tumor, and stromal tumor; esophageal cancers such as but not limited to, squamous cancer, adenocarcinoma, adenoid cystic carcinoma, mucoepidermoid carcinoma, adenosquamous carcinoma, sarcoma, melanoma, plasmacytoma, verrucous carcinoma, and oat cell (small cell) carcinoma; stomach cancers such as but not limited to, adenocarcinoma, fungating (polypoid), ulcerating, superficial spreading, diffusely spreading, malignant lymphoma, liposarcoma, fibrosarcoma, and carcinosarcoma; colon cancers; rectal cancers; liver cancers such as but not limited to hepatocellular carcinoma and hepatoblastoma; gallbladder cancers such as adenocarcinoma; cholangiocarcinomas such as but not limited to papillary, nodular, and diffuse; lung cancers such as non-small cell lung cancer, squamous cell carcinoma (epidermoid carcinoma), adenocarcinoma, large-cell carcinoma and small-cell lung cancer; testicular cancers such as but not limited to germinal tumor, seminoma, anaplastic, classic (typical), spermatocytic, nonseminoma, embryonal carcinoma, teratoma carcinoma, choriocarcinoma (yolk-sac tumor), prostate cancers such as but not limited to, prostatic intraepithelial neoplasia, adenocarcinoma, leiomyosarcoma, and rhabdomyosarcoma; penal cancers; oral cancers such as but not limited to squamous cell carcinoma; basal cancers; salivary gland cancers such as but not limited to adenocarcinoma, mucoepidermoid carcinoma, and adenoidcystic carcinoma; pharynx cancers such as but not limited to squamous cell cancer, and verrucous; skin cancers such as but not limited to, basal cell carcinoma, squamous cell carcinoma and melanoma, superficial spreading melanoma, nodular melanoma, lentigo malignant melanoma, acral lentiginous melanoma; kidney cancers such as but not limited to renal cell carcinoma, adenocarcinoma, hypemephroma, fibrosarcoma, transitional cell cancer (renal pelvis and/or uterer); Wilms' tumor; bladder cancers such as but not limited to transitional cell carcinoma, squamous cell cancer, adenocarcinoma, carcinosarcoma. In addition, cancers include myxosarcoma, osteogenic sarcoma, endotheliosarcoma, lymphangioendotheliosarcoma, mesothelioma, synovioma, hemangioblastoma, epithelial carcinoma, cystadenocarcinoma, bronchogenic carcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma and papillary adenocarcinomas (for a review of such disorders, see Fishman et al., 1985, Medicine, 2d Ed., J.B. Lippincott Co., Philadelphia and Murphy et al., 1997, Informed Decisions: The Complete Book of Cancer Diagnosis, Treatment, and Recovery, Viking Penguin, Penguin Books U.S.A., Inc., United States of America).

The prophylactically and/or therapeutically effective regimens are also useful in the treatment, prevention and/or management of a variety of cancers or other abnormal proliferative diseases, including (but not limited to) the following: carcinoma, including that of the bladder, breast, colon, kidney, liver, lung, ovary, pancreas, stomach, cervix, thyroid and skin; including squamous cell carcinoma; hematopoietic tumors of lymphoid lineage, including leukemia, acute lymphocytic leukemia, acute lymphoblastic leukemia, B-cell lymphoma, T cell lymphoma, Burkitt's lymphoma; hematopoietic tumors of myeloid lineage, including acute and chronic myelogenous leukemias and promyelocytic leukemia; tumors of mesenchymal origin, including fibrosarcoma and rhabdomyoscarcoma; other tumors, including melanoma, seminoma, tetratocarcinoma, neuroblastoma and glioma; tumors of the central and peripheral nervous system, including astrocytoma, neuroblastoma, glioma, and schwannomas; tumors of mesenchymal origin, including fibrosarcoma, rhabdomyoscarama, and osteosarcoma; and other tumors, including melanoma, xeroderma pigmentosum, keratoactanthoma, seminoma, thyroid follicular cancer and teratocarcinoma. In some embodiments, cancers associated with aberrations in apoptosis are prevented, treated and/or managed in accordance with the methods of the invention. Such cancers may include, but not be limited to, follicular lymphomas, carcinomas with p53 mutations, hormone dependent tumors of the breast, prostate and ovary, and precancerous lesions such as familial adenomatous polyposis, and myelodysplastic syndromes. In specific embodiments, malignancy or dysproliferative changes (such as metaplasias and dysplasias), or hyperproliferative disorders of the skin, lung, liver, bone, brain, stomach, colon, breast, prostate, bladder, kidney, pancreas, ovary, and/or uterus are prevented, treated and/or managed in accordance with the methods of the invention. In other specific embodiments, a sarcoma, melanoma, or leukemia is prevented, treated and/or managed in accordance with the methods of the invention. In certain embodiments, the subjects have acute myelogenous leukemia (AML). In certain other embodiments, the subjects have myelodysplastic syndrome (MDS). In other embodiments, the subjects have chronic myelomonocytic leukemia (CMML). In other specific embodiments, myelodysplastic syndrome is prevented, treated and/or managed in accordance with the methods of the invention.

A major objective in treatment of cancers is to be able to target the tumor with sufficient levels of the appropriate therapeutic without systemic toxicity.

In certain embodiments, the method of treating cancer includes: (i) a reduction of cancer cells, (ii) absence of increase of cancer cells; (iii) a decrease in viability of cancer cells; (iv) decrease in growth of cancer cells, in a subject.

In certain embodiments, the subject that is treated with the present method of the disclosure has been diagnosed with the disease and has undergone therapy. In certain embodiments, the subject that is treated with the present method of the disclosure has been diagnosed with cancer and has undergone cancer therapy.

In certain embodiments, the subject is in remission from cancer. In certain embodiments, the subject has relapsed from cancer. In certain embodiments, the subject has failed cancer treatment.

Provided herein are articles of manufacture and kits containing materials useful for treating the conditions described herein. The article of manufacture may include a container of a compound as described herein with a label. Suitable containers include, for example, bottles, vials, and test tubes. The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition having a vaccine which is effective for treating or preventing cancer. The label on the container may indicate that the composition is useful for treating specific conditions and may also indicate directions for administration.

In one or more embodiments, the present invention can provide for a kit comprising a therapeutically effective amount of vaccine. It is to be understood that any of the embodiments of the vaccine can be included in one or more kits in accordance with one or more implementations of the present disclosure.

5.9 Immune Response

Comparison of the immune response raised in a subject by the polypeptide with the immune response raised by the full length protein may be carried out by any means available to one of skill in the art. One simple method as used in the examples below involves immunization of a model subject such as mouse and then challenge with a lethal dose of E. coli. For proper comparison, one of skill in the art would naturally select the same adjuvant such as Freund's complete adjuvant. In such a test the immunogenic polypeptide fragments of the present invention will raise a substantially similar immune response in a subject (i.e., will provide substantially the same protection against the lethal challenge) if, for example, the polypeptide provides at least 70% of the protection provided by the full length protein, at least 80% of the protection provided by the full length protein, at least 85% of the protection provided by the full length protein, at least 90% of the protection provided by the full length protein, at least 95% of the protection provided by the full length protein, at least 97% of the protection provided by the full length protein, at least 98% of the protection provided by the full length protein, or at least 99% of the protection provided by the full length protein.

The compositions of the invention may elicit both a cell mediated immune response as well as a humoral immune response. This immune response will preferably induce long lasting (e.g. neutralising) antibodies and a cell mediated immunity that can quickly respond upon reexposure to the antigen.

Two types of T cells, CD4 and CD8 cells, are generally thought necessary to initiate and/or enhance cell mediated immunity and humoral immunity. CD8 T cells can express a CD8 co-receptor and are commonly referred to as Cytotoxic T lymphocytes (CTLs). CD8 T cells are able to recognized or interact with antigens displayed on MHC Class 1 molecules.

CD4 T cells can express a CD4 co-receptor and are commonly referred to as T helper cells. CD4 T cells are able to recognize antigenic peptides bound to MHC class II molecules. Upon interaction with a MHC class II molecule, the CD4 cells can secrete factors such as cytokines.

These secreted cytokines can activate B cells, cytotoxic T cells, macrophages, and other cells that participate in an immune response.

6. EXAMPLES 6.1 Generation of Fusion Proteins

In one embodiment, Sindbis fusion protein is generated by baculovirus expression in Sf9 insect cells. Since baculoviruses can only infect specific invertebrate species, they are nonpathogenic to mammals. Unlike bacterial protein expression, proteins expressed in the baculovirus system are processed, folded, and modified similarly to those produced in a mammalian expression system. Additionally, baculovirus-expressed proteins are easily scaled up to produce large quantities of recombinant protein. Insect cell lines are available that grow well in suspension cultures, allowing the production of recombinant proteins in large-scale bioreactors. While both insect and mammalian cells are capable of making N-linked glycosylations, the specific glycosylation pathway is different. N-glycans produced in insect cells can have either a high-mannose or paucimannosidic structure, both of which have terminal mannose residues. N-glycans produced in mammalian cells can have either a high-mannose structure or a complex structure terminating in galactose and sialic acid. Binding of SINV to the dendritic cell (“DC”) receptor (Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin) DC-SIGN requires high mannose glycosylation of its envelope glycoproteins. Virus produced in mammalian cells will not bind DC-SIGN without additional enzymatic modifications. Therefore, production of fusion protein in insect cells achieves efficient targeting of the TAA to the DC.

The gene encoding the VGP is produced through gene synthesis and codon-optimized for insect cell expression. The recombinant fusion protein is composed of the ectodomains of the pE2 and E1 Sindbis glycoproteins connected by a flexible linker and linked to a TAA by a second linker (see FIG. 4). In one embodiment, TAA is NY-ESO-1. In certain embodiment, other TAAs are inserted into the coding sequence. Alternatively, a construct is generated with two or more TAAs in tandem, which results in a more potent immune response. The E3 component of pE2 acts as a signal peptide for secretion of the protein, assists in the binding of E1 and E2, and is naturally cleaved from the mature protein by furin. Alphavirus glycoproteins are produced as the mature secreted protein forming a trimer of the heterodimeric complex of E2 and E1, which mimic the trimeric glycoprotein spike observed on the SINV envelope. The second flexible linker allows proper folding of NY-ESO-1 without interfering with the multimerization of E2/E1. Additionally, since the first 80 amino acids of NY-ESO-1 are glycine-rich and largely devoid of T cell antigens, in one embodiment, only amino acids residues 81-180 have been included in the construct. In certain embodiments, the TAA comprises amino acid residues 1-180, 81-100, 100-150, 150-180 of NY-ESO-1. A His-tag has been added to the C-terminus of the protein for purification purposes. The novel protein is analyzed to determine its multimeric structure by non-denaturing gel and size-exclusion chromatography. Further, ELISA and western blot assays specific for the protein are developed. The protein has several antigenic targets (NY-ESO-1, His-tag, and SINV E1 and E2) that are detected with commercial antibodies.

Provided herewith is a viral glycoprotein complex which is a recombinant protein consisting of the ectodomains E3, E2, and E1 proteins of the Sindbis virus linked to a truncated peptide derived from the tumor-associated antigen NY-ESO-1. The amino acid sequences for the Sindbis virus structural proteins E3, E2, 6K, and E1 (NCBI website reference sequence NP_062890.1). Transmembrane domains of E2 and E1 proteins were removed from the coding sequence. The E2 and E1 proteins were joined by a flexible glycine/serine linker (GGGGSGGGGSGGGGSGGGG)(SEQ ID NO: 13) in place of the 6K region. The amino acid sequence for NY-ESO-1 (NCBI website reference sequence NP_001318.1). As N-terminus of NY-ESO-1 is very glycine-rich and largely devoid of T cell antigens, in one embodiment, the first 78 amino acids of the protein were deleted. In one embodiment, the Sindbis E3/E2/E1 sequence was linked to the truncated 102 amino acid NY-ESO-1 protein by a TEV cleavage site (ENLYFQ)(SEQ ID NO: 14) and a second glycine/serine linker (GGGGGSGGGGSGGGGS)(SEQ ID NO: 15). In one embodiment, a 6×-His tag was added to the C-terminus of the recombinant protein for purification purposes. The DNA sequence encoding the recombinant protein was synthesized by Genscript (Piscataway, N.J.) and codon optimized for expression in Sf9 cells. The DH10Bac strain was used for recombinant bacmid generation. Sf9 insect cells were transfected with bacmid using Cellfectin II and incubated in Sf-900 II medium for 5-7 days at 27° C. The supernatant after centrifugation was collected and designated as P1 viral stock. Cells were further infected with P1 to generate high titer P2 stock. Sf9 cells were transfected with P2 virus and media was collected 72 hours later. Supernatant was dialyzed against 50 mM Tris, 150 mM NaCl, pH8.0 containing protease inhibitor, and protein was purified with a Ni column and analyzed by anti-His western blot.

6.2 Receptor Binding Analysis

SINV binds to receptors on both tumor cells (laminin receptor) and dendritic cells (DC-SIGN). The fusion protein, maintaining the conformational shape of the E2/E1 heterodimeric trimer on the surface of the virus, binds to these same receptors. For DC-SIGN binding, an assay using protein A microbeads and DC-SIGN Fc fusion protein are used. Fusion protein binds to beads maximally coated with DC-SIGN, then a fluorescently labelled secondary antibody for the VGP (anti-His or anti-NY-ESO-1) is used for detection by flow cytometry. Binding is analyzed at multiple protein concentrations and comparing to other DC-SIGN-targeting methods such as anti-DC-SIGN antibodies. Using a flow cytometer equipped with a 96-well plate reader, these assays can be performed in high throughput fashion. Viral proteins target antigens to DC with similar affinity to antibodies for DC-SIGN. Additionally, binding of the fusion protein to DC is analyzed from both humans (expressing DC-SIGN) and mouse (L-SIGN). Receptor-blocking antibodies and mannan, a mannose polysaccharide, are used to demonstrate the specificity of the interaction. For laminin receptor binding, the binding is analyzed using multiple tumor cell lines with varying degrees of laminin receptor expression. This binding can be blocked using an antibody to the laminin receptor or with excess laminin, the natural ligand for the receptor. The fusion protein preferentially binds these cells over bystander cells and effectively delivers a tumor-associated antigen to DC for processing and presentation.

6.3 In Vitro Assays

SINV boosts the immune system's response to tumor cells through NK cell recruitment and activation of T cells against tumor associated antigens encoded by the virus. The latter of these effects is accomplished by delivery of antigen to DC by the virus through the DC-SIGN receptor. In order to induce a strong T cell response, the DC must first become activated through the detection of pathogen-associated molecular patterns (PAMPs) that are common among viruses, bacteria, or parasites. Activated DC express increased levels of MHC molecules as well as the costimulatory molecules B7-1 and B7-2. It is therefore necessary to assess whether the recombinant fusion protein has sufficient immunogenicity to induce DC activation or if it is necessary to couple it to an adjuvant.

From human peripheral blood mononuclear cells (PBMC), pure populations of specific immune cell types are obtained by magnetic bead selection, then the direct effect that the VGP/NY-ESO-1 is evaluated. Activation of DC and NK cells can be measured by flow cytometric analysis of activation markers on the cell surface and the detection of cytokine secretion by ELISA. The ability to modulate a tumor-specific response is assessed using T cells obtained from cancer patients. These patients have been exposed to the tumor antigen and have an elevated percentage of tumor-specific T cells compared to healthy donors. DC from the patient is treated with the recombinant fusion protein overnight, during which time, the protein is absorbed, processed, and relevant epitopes are presented on the cell surface. DC is co-cultured with patient T cells for several days, at which point the T cells will be analyzed for an antigen-specific response. Using CFSE-labeled T cells, T cell proliferation is measured by flow cytometry. An ELISPOT assay is used to detect activated NY-ESO-1-specific T cells. NY-ESO-1-specific T cells produce IFNγ upon recognition of their specific epitope presented by the DC, which are captured for detection by antibodies coating the wells of the ELISPOT plate. These assays demonstrates that peptides from the fusion protein are processed and presented by the dendritic cells and T cell response is stimulated in humans.

While we believe that the most important effect of the VGP treatment is through activation of the immune system, the role of direct tumor targeting through the laminin receptor should not be discounted. SINV induces apoptosis in tumor cells upon entry and in the absence of viral replication. The effects the VGP has on tumor cell growth and survival is investigated in vitro. Several tumor cell lines with varying levels of laminin receptor expression is used to evaluate what role if any direct protein-tumor interaction has on the efficacy of the treatment.

6.4 In Vivo Stimulation Assays

Before attempting to treat an actively growing tumor, it is important to demonstrate induction of a tumor-specific immune response in vivo with VGP/NY-ESO-1. Normal mice have not encountered NY-ESO-1 and it is recognized by the immune system as a foreign antigen Immunization of mice with the VGP/NY-ESO-1 by ip injection results in activation and proliferation of NY-ESO-1-specific T cells as well as fusion protein-specific T cells as well as NK cell activation. To establish efficacy of this treatment, VGP/NY-ESO-1 shows greater immunogenicity than the VGP alone, NY-ESO-1 alone, and anti-DC-SIGN/NY-ESO-1 (controls). The checkpoint inhibitors anti-CTLA-4 and PD-1 shows strong immunotherapeutic potential and works synergistically with the disclosed therapy for an even stronger immune response. The effects of the presently disclosed treatment with and without co-administration of these blocking antibodies is evaluated.

Based on known MHC binding preferences, epitopes from NY-ESO-1 and the VGP are presented by the MHC molecules of a particular mouse strain. Alternatively, transgenic mice expressing human MHC molecules, for which NY-ESO-1 epitopes are known, can be used. Samples from blood, spleen, and draining lymph nodes are taken to check for immune stimulation. MHC tetramer staining are used to verify the presence of an expanded population of NY-ESO-1 and VGP-specific T cells. These cells exist in naïve mice but in minute amounts below the detection threshold. In a successful immunization, these cells proliferate and are readily detectable by flow cytometry. Additionally, flow cytometry is used to analyze the activation state of these tetramer+ cells, by looking at surface markers such as CD62L and CD69, which are present only on naïve and activated cells, respectively. While activation of VGP-specific T cells is considered an off-target effect, it further improves the immune response to the tumor, as these antigens would also be targeted to the tumor itself.

ELISPOT assays are used to determine that these NY-ESO-1-specific T cells have effector function. CD8+ T cells harvested from the spleen and lymph nodes of immunized mice are co-cultured with antigen-presenting cells preloaded with NY-ESO-1. Activated T cells specific for these epitopes produce cytokines such as IFNγ in response, which are captured by antibodies coating the bottom of the well for detection. The effector function of these activated T cells is analyzed by performing a cytotoxicity assay. Similar to the ELISPOT assay, CD8+ T cells from immunized mice are co-cultured with antigen presenting cells preloaded with relevant peptides. Alternatively, a syngeneic murine cell line transduced with lentivirus to express NY-ESO-1 is used. Activated CD8+ CTL directly kill these NY-ESO-1-presenting cells, and the cytotoxicity is measured by detection of intracellular proteins from the lysed cells such as lactate dehydrogenase in the supernatant.

The effect of the therapy on other immune cell populations is analysed, which can be accomplished by flow cytometry. Specifically, the effects of the treatment on the percentage of several immune cell types (CD4+ and CD8+ T cells, DC, NK cells, B cells, macrophages) with respect to one another, as well as the total cell number are analysed. Antibodies generated by the mouse against the recombinant protein is evaluated by analyzing blood serum. Plasma cells generate antibodies specific for NY-ESO-1 and the VGP. In certain embodiments, when multiple doses are adminstered, these antibodies may interfere with the effectiveness of the therapy. In certain embodiments, the antibodies aid in tumor clearance as these antigens are targeted to the tumor itself, making it more antigenic.

The proper dosing strategy (amount of protein, number of doses, frequency of doses) is examined to generate a strong anti-tumor immune response before proceeding into a tumor model. Additionally, ELISA is developed to detect the VGP in mouse serum and tissues to evaluate dosing as well as protein trafficking and stability in vivo.

In order to properly activate T cells, DC are activated through the detection of pathogen associated molecular patterns (PAMPs). In certain embodiments, VGP/NY-ESO-1 is coupled with an adjuvant to increase its immunogenicity.

LIST OF REFERENCES

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The present invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description and the accompanying figures. Such modifications are intended to fall within the scope of the appended claims.

Patents, patent applications, and publications are cited throughout this application, the disclosures of which, particularly, including all disclosed chemical structures, are incorporated herein by reference. Citation of the above publications or documents is not intended as an admission that any of the foregoing is pertinent prior art, nor does it constitute any admission as to the contents or date of these publications or documents. All references cited herein are incorporated by reference to the same extent as if each individual publication, patent application, or patent, was specifically and individually indicated to be incorporated by reference.

The foregoing written specification is considered to be sufficient to enable one skilled in the art to practice the invention. Various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and fall within the scope of the appended claims. 

1. An isolated or recombinant fusion protein consisting essentially of alpha virus surface membrane glycoproteins E1, E2 and optionally E3, a linker and at least one tumor associated antigen, wherein the fusion protein stimulates an immune response when administered to a subject.
 2. The fusion protein of claim 1 comprising an amino acid sequence having at least 98% identity to SEQ ID NO:
 1. 3. The fusion protein of claim 1 comprising at least amino acid residues at positions 66-978 of SEQ ID NO:1.
 4. The fusion protein of claim 2 further comprising a deletion of amino acid residues at (i) positions 1-65; (ii) positions 979-984; or (iii) positions 1-65 and 979-984, of SEQ ID NO:1.
 5. The fusion protein of claim 1 encoded by a nucleic acid molecule having at least 95% identity to SEQ ID NO:
 2. 6. The fusion protein of claim 1 wherein E2 comprises an amino acid sequence that is at least 300 amino acid in length and has at least 95% sequence identity to SEQ ID NO:1 at positions 66-429.
 7. The fusion protein of claim 1 wherein E1 comprises an amino acid sequence that is at least 300 amino acid in length and has at least 95% sequence identity to SEQ ID NO:1 at positions 449-854.
 8. The fusion protein of claim 1, wherein the tumor associated antigen is a polypeptide fragment that is at least 10 consecutive amino acids of any of SEQ ID NOS: 3-11, wherein the polypeptide fragment comprises at least 10 consecutive amino acids is immunogenic and the immunogenic polypeptide fragment comprises less than 1100 amino acids of the polypeptide of SEQ ID Nos: 3-11.
 9. A vaccine comprising the fusion protein of claim 1 capable of eliciting an immune response through NK cells, T-cells, or memory T-cells in a subject.
 10. A composition comprising the fusion protein of claim 1 and a pharmaceutically acceptable carrier.
 11. The composition of claim 10 further comprising an adjuvant.
 12. An expression vector comprising a nucleic acid molecule encoding the fusion protein of claim
 1. 13. A cell comprising the expression vector of claim 12 wherein the cell expresses a fusion protein.
 14. The fusion protein of claim 1 wherein the tumor associated antigen is a polypeptide fragment of a protein listed in table 3 of the NCI Pilot Project to Prioritize Cancer Antigens described in Clin Cancer Res 2009; 15:5323-5337.
 15. The fusion protein of claim 1 which is expressed as one contiguous gene product.
 16. The fusion protein of claim 1 which is capable of forming a dimer or trimer.
 17. The fusion protein of claim 1 wherein the at least one tumor associated antigen is inserted internally to the alpha virus surface membrane glycoprotein E1 or E2.
 18. The fusion protein of claim 1 wherein the at least one tumor associated antigen is linked terminally to the alpha virus surface membrane glycoprotein E1 or E2.
 19. The fusion protein of claim 1 further conjugated to a Capsid protein.
 20. The fusion protein of claim 1 wherein the alpha virus surface membrane glycoprotein is Sindbis alpha virus protein.
 21. A method for inducing or modulating an immune response in a subject, comprising administering to the subject a fusion protein wherein the fusion protein consists essentially of alpha virus surface membrane glycoprotein E1 and/or E2 conjugated to one or more tumor associated antigen via at least one linker.
 22. A method of treating latent viral infections including HIV, Shingles and Herpes in a subject, comprising administering to the subject a fusion protein wherein the fusion protein consists essentially of alpha virus surface membrane glycoprotein E1 and/or E2 conjugated to one or more viral antigens via at least one linker.
 23. The method of claim 21 wherein E2 comprises an amino acid sequence that is at least 300 amino acid in length and has at least 95% sequence identity to SEQ ID NO:1 at positions 66-429.
 24. The method of claim 21 wherein E1 comprises an amino acid sequence that is at least 300 amino acid in length and has at least 95% sequence identity to SEQ ID NO:1 at positions 449-854.
 25. A method to produce a fusion protein comprising expressing the fusion protein in an expression vector comprising a nucleotide construct encoding: (a) alpha virus surface membrane glycoprotein E1 and/or E2; (b) at least one tumor associated antigen or viral antigen, wherein the tumor associated antigen or viral antigen is operatively linked to the alpha virus surface membrane glycoprotein E1 and/or E2, wherein the fusion protein stimulates an immune response when administered to a subject.
 26. A method for treating cancer in a subject, comprising administering to the subject in need thereof, a fusion protein wherein the fusion protein consists essentially of alpha virus surface membrane glycoprotein E1, E2 and at least one linker, wherein the fusion protein stimulates an immune response when administered to the subject.
 27. The method of claim 25 wherein the tumor associated antigen is a polypeptide fragment that is at least 10 consecutive amino acids of any of SEQ ID NOS: 3-11, wherein the polypeptide fragment comprises at least 10 consecutive amino acids is immunogenic and the immunogenic polypeptide fragment comprises less than 1100 amino acids of the polypeptide of SEQ ID Nos: 3-11.
 28. The method of claim 25 wherein the fusion protein is produced in a mammalian cell system.
 29. The method of claim 25 wherein the fusion protein is produced in insect cells.
 30. The method of claim 25 wherein the fusion protein is expressed in a baculovirus vector and the fusion protein is expressed in insect cells.
 31. The method of claim 21 further comprising administering an additional therapy. 